& Frequently Asked Questions: Data File Formats
General formats:
ENCODE-specific formats:
Download only formats:
& BED format
BED format provides a flexible way to define the data lines that
are displayed in an annotation track. BED lines have three required fields and
nine additional optional fields. The number of fields per line must be consistent
throughout any single set of data in an annotation track. The order of the
optional fields is binding: lower-numbered fields must always be populated if
higher-numbered fields are used.
If your data set is BED-like, but it is very large (over 50MB) and you would like to keep
it on your own server, you should use the
data format.
The first three required BED fields are:
chrom - The name of the chromosome (e.g. chr3, chrY,
chr2_random) or scaffold (e.g. scaffold10671).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99.
The 9 additional optional BED fields are:
name - Defines the name of the BED line.
This label is
displayed to the left of the BED line in the Genome Browser
window when the track is open to full display mode or directly to the
left of the item in pack mode.
score - A score between 0 and 1000. If the track line
useScore attribute is set to 1 for this annotation data set, the
score value will determine the level of gray in which
this feature is displayed (higher numbers = darker gray).
This table shows the Genome Browser's translation of BED score values into
shades of gray:
score in range&&
strand - Defines the strand - either '+' or '-'.
thickStart - The starting position at which the feature
is drawn thickly (for example, the start codon in gene
displays). When there is no thick part, thickStart and thickEnd are
usually set to the chromStart position.
thickEnd - The ending position at which the feature is
drawn thickly (for example, the stop codon in gene displays).
itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0).
If the track line itemRgb attribute is set to &On&,
this RBG value will determine the display color of the data contained
in this BED line. NOTE: It is recommended that a simple color scheme
(eight colors or less) be used with this attribute to avoid
overwhelming the color resources of the Genome Browser and your
Internet browser.
blockCount - The number of blocks (exons) in the
blockSizes - A comma-separated list of the block
sizes. The number of items in this list should correspond to
blockCount.
blockStarts - A comma-separated list of block starts.
All of the blockStart positions should be calculated relative to
chromStart. The number of items in
this list should correspond to blockCount.
In BED files with block definitions, the first blockStart value must
be 0, so that the first block begins at chromStart.
Similarly, the final
blockStart position plus the final blockSize value must equal
Blocks may not overlap.
Here's an example of an annotation track that uses a complete BED definition:
track name=pairedReads description=&Clone Paired Reads& useScore=1
cloneA 960 +
2 567,488, 0,3512
cloneB 900 -
2 433,399, 0,3601
This example shows an annotation track that uses the itemRgb attribute to
individually color each data line. In this track, the color scheme distinguishes
between items named &Pos*& and those named &Neg*&. See the
usage note in the itemRgb description above for color palette
restrictions.
NOTE: The track and data lines in this example have been reformatted for
documentation purposes. This
can be pasted into the browser without editing.
browser position chr7:7495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2
itemRgb="On"
to display this track in the Genome Browser.
It is also possible to color items by strand in a BED track
using the colorByStrand attribute in the
below. For BED tracks, this attribute functions only for custom tracks
with 6 to 8 fields (i.e. BED6 through BED8).
NOTE: The track and data lines in this example have been reformatted for
documentation purposes. This
can be pasted into the browser without editing.
browser position chr7:7495720
browser hide all
track name="ColorByStrandDemo" description="Color by strand demonstration"
visibility=2 colorByStrand="255,0,0 0,0,255"
to display this track in the Genome Browser.
& bigBed format
The bigBed format stores annotation items that can either be simple, or a
linked collection of exons, much as
BigBed files are created initially from bed type files,
using the program bedToBigBed.
resulting bigBed files are in an indexed binary format.
The main advantage of
the bigBed files is that only the portions of the files needed to display a
particular region are transferred to UCSC, so for large data sets bigBed is
considerably faster than regular bed files.
The bigBed file remains on
your web accessible server (http, https, or ftp), not on the UCSC server.
for more information
on the bigBed format.
& BED detail format
This is an extension of BED format. BED detail uses the first 4 to
12 columns of BED format, plus 2 additional fields that are used to enhance
the track details pages.
The first additional field is an ID, which can be
used in place of the name field for creating links from the details pages.
second additional field is a description of the item, which can be a long
description and can consist of html, including tables and lists.
Requirements for BED detail custom tracks are: fields must be
tab-separated, &type=bedDetail& must be included in the
and the name and position fields should uniquely describe items so that the
correct ID and description will be displayed on the details pages.
This example uses the first 4 columns of BED format, but up to 12 may be used.
to view this track in the Genome Browser.
track name=HbVar type=bedDetail description="HbVar custom track" db=hg19 visibility=3 url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$"
chr11	;;Hb_North_York	2619	Hemoglobin variant
chr11	;;HBD c.1 G>A	2659	delta0 thalassemia
chr11	;;Hb Sheffield	2672	Hemoglobin variant
chr11	;;Hb A2-Lyon	2676	Hemoglobin variant
chr11	;;Hb Aix-les-Bains	2677	Hemoglobin variant
& bedGraph format
The bedGraph format allows display of continuous-valued data in track
format. This display type is useful for probability scores and transcriptome
data. This track type is similar to the
format, but unlike the WIG format, data
exported in the bedGraph format are preserved in their original state. This
can be seen on export using the table browser. For more information about
the bedGraph format, please see the
details page.
If you have a very large data set and you would like to keep it on your own
server, you should use the
& PSL format
PSL lines represent alignments, and are typically taken from files generated by BLAT
or psLayout. See the
documentation for more details. All of the following fields are
required on each data line within a PSL file:
matches - Number of bases that match that aren't repeats
misMatches - Number of bases that don't match
repMatches - Number of bases that match but are part of repeats
nCount - Number of 'N' bases
qNumInsert - Number of inserts in query
qBaseInsert - Number of bases inserted in query
tNumInsert - Number of inserts in target
tBaseInsert - Number of bases inserted in target
strand - '+' or '-' for query strand. For translated alignments, second '+'or '-' is for genomic strand
qName - Query sequence name
qSize - Query sequence size
qStart - Alignment start position in query
qEnd - Alignment end position in query
tName - Target sequence name
tSize - Target sequence size
tStart - Alignment start position in target
tEnd - Alignment end position in target
blockCount - Number of blocks in the alignment (a block contains no gaps)
blockSizes - Comma-separated list of sizes of each block
qStarts - Comma-separated list of starting positions of each block in query
tStarts - Comma-separated list of starting positions of each block in target
Here is an example of an annotation track in PSL format. Note that line
breaks have been inserted into the PSL lines in this example for
documentation display purposes. This
can be pasted into the browser without editing.
browser position chr22:74000
browser hide all
track name=fishBlats description=&Fish BLAT& visibility=2
useScore=1
59 9 0 0 1 823 1 96 +- FS_CONTIG_5 171 1062 chr22
53 2 48,20,
59 7 0 0 1 55 1 55 +- FS_CONTIG_5
47 2 21,45,
59 7 0 0 1 55 1 55 -+ FS_CONTIG_5
48 2 45,21,
to display this track in the Genome Browser.
Be aware that the coordinates for a negative strand in a PSL line are handled in a special way. In the
qStart and qEnd fields, the coordinates indicate the position where the query matches from
the point of view of the forward strand, even when the match is on the reverse strand.
However, in the qStarts list, the coordinates are reversed.
Here is a 61-mer containing 2 blocks that align on the minus strand and
2 blocks that align on the plus strand (this sometimes happens due to assembly errors):
6 tens position in query
0 ones position in query
++++++++++++++
+++++ plus strand alignment on query
------------------
--------------------
minus strand alignment on query
0 ones position in query negative strand coordinates
0 tens position in query negative strand coordinates
Plus strand:
blockSizes=14,5
qStarts=22,56
Minus strand:
blockSizes=20,18
qStarts=5,39
Essentially, the minus strand blockSizes and qStarts are
what you would get if you reverse-complemented the query.
However, the qStart and qEnd are not reversed. Use the following formulas to convert one to the other:
Negative-strand-coordinate-qStart = qSize - qEnd
= 61 - 56 =
Negative-strand-coordinate-qEnd
= qSize - qStart = 61 -
BLAT this actual sequence against hg19 for a real-world example:
GGGTAAAATGAGTTTTTT
GGTCCAATCTTTTA
ATCCACTCCCTACCCTCCTA
Look for the alignment on the negative strand (-) of chr21, which
conveniently aligns to the window chr21:10,000,001-10,000,061.
Browser window coordinates are 1-based [start,end] while psl coordinates are 0-based [start,end), so a start of 10,000,001
in the browser corresponds to a start of 10,000,000 in the psl. Subtracting 10,000,000 from the target (chromosome) position
in psl gives the query negative strand coordinate above.
The 4, 14, and 5 bases at beginning, middle, and end were
chosen to not match with the genome at the corresponding position.
& GFF format
GFF (General Feature Format) lines are based on the Sanger
. GFF lines have nine required fields that must be
tab-separated. If the fields are separated by spaces instead of tabs, the track will not
display correctly. For more information on GFF format, refer to Sanger's
Note that there is also a GFF3 specification that is not currently supported by the Browser.
All GFF tracks must be formatted according to Sanger's GFF2 specification.
If you would like to obtain browser data in GFF (GTF) format, please refer to
on the Wiki.
Here is a brief description of the GFF fields:
seqname - The name of the sequence.
Must be a chromosome or scaffold.
source - The program that generated this feature.
feature - The name of this type of feature. Some examples of
standard feature types are "CDS", "start_codon", "stop_codon", and
start - The starting position of the feature in the sequence.
The first base is numbered 1.
end - The ending position of the feature (inclusive).
score - A score between 0 and 1000. If the track line
useScore attribute is set to 1 for this annotation data set, the
score value will determine the level of gray in which
this feature is displayed (higher numbers = darker gray). If there is no
score value, enter ".".
strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the
first base.
If the feature is not a coding exon, the value should be '.'.
group - All lines with the same group are linked together into a single item.
Here's an example of a GFF-based track.
can be pasted into the browser without editing. NOTE: Paste operations on some
operating systems will replace tabs with spaces, which will result in an error
when the GFF track is uploaded. You can circumvent this problem by pasting the
URL of the above example
(http://genome.ucsc.edu/goldenPath/help/regulatory.txt) instead of the text
itself into the custom annotation track text box. If you encounter an error
when loading a GFF track, check that the data lines contain tabs rather than
browser position chr22:25000
browser hide all
track name=regulatory description=&TeleGene(tm) Regulatory Regions&
visibility=2
TeleGene enhancer
TeleGene promoter
TeleGene promoter
to display this track in the Genome Browser.
& GTF format
GTF (Gene Transfer Format) is a refinement to GFF that tightens the specification.
The first eight GTF fields are the same as GFF. The group field has been
expanded into a list of attributes.
Each attribute consists of a type/value pair.
Attributes
must end in a semi-colon, and be separated from any following attribute by exactly one space.
The attribute list must begin with the two mandatory attributes:
gene_id value - A globally unique identifier for the genomic
source of the sequence.
transcript_id value - A globally unique identifier for the
predicted transcript.
Example:Here is an example of the ninth field in a GTF data line:
&&&&gene_id "Em:U6.mRNA"; transcript_id "Em:U6.mRNA";
exon_number 1
The Genome Browser groups together GTF lines that have the same
transcript_id value.
It only looks at features of type exon and
For more information on this format, see .
If you would like to obtain browser data in GTF format, please refer to
on the Wiki.
& HAL format
HAL is a graph-based structure to efficiently store and index multiple genome alignments and ancestral
reconstructions. HAL files are represented in ,
an open standard for storing and indexing large, compressed scientific data sets. Genomes within HAL are organized according
to the phylogenetic tree that relate them: each genome is segmented into pairwise DNA alignment blocks
with respect to its parent and children (if present) in the tree. Note that if the phylogeny is unknown,
a star tree can be used. The modularity provided by this tree-based decomposition allows for efficient querying
of sub-alignments, as well as the ability to add, remove and update genomes within the alignment
with only local modifications to the structure. Another important feature of HAL is reference
independence: alignments in this format can be queried with respect to the coordinates of any genome they contain.
HAL files can be created or read with a comprehensive C++ API (click
for source code and manual). A set of command line tools is included to perform basic operations, such as importing and exporting data,
identifying mutations, coordinate mapping (liftOver), and comparative assembly hub generation.
HAL is the native output format of the Progressive Cactus alignment pipeline, and is
included in the
installation package.
& MAF format
The multiple alignment format stores a series of
multiple alignments in a format that is easy to
parse and relatively easy to read.
This format
stores multiple alignments at the DNA level
between entire genomes. Previously used formats
are suitable for multiple alignments of single proteins or
regions of DNA without rearrangements, but would require
considerable extension to cope with genomic issues such as
forward and reverse strand directions, multiple pieces
to the alignment, and so forth.
General Structure
The .maf format is
line-oriented. Each multiple alignment ends with a
blank line.
Each sequence in an alignment is on a single
line, which can get quite long, but there is no length limit.
Words in a line are delimited by any white space. Lines
starting with # are considered to be comments.
Lines starting with ## can be ignored by most
programs, but contain meta-data of one form or
The file is divided into paragraphs that terminate
in a blank line.
Within a paragraph, the first
word of a line indicates its type.
Each multiple
alignment is in a separate paragraph that begins
with an &a& line and contains an &s& line
for each sequence in the multiple alignment.
Some MAF files may contain other
optional line types:
an "i" line containing information about what is in the
aligned species DNA before and after the immediately
preceding "s" line
an "e" line containing information about the size of the
gap between the alignments that span the current
a "q" line indicating the quality of each aligned base
for the species
Parsers may ignore any other types of paragraphs and
other types of lines within an alignment paragraph.
Custom Tracks
The first line of a custom MAF track must be a "track" line
that contains a name=value pair specifying the track name.
Here is an example of a minimal track line:
track name=sample
The following variables can be specified in the track line
of a custom MAF:
name=sample - Required. Name the track
description="Sample Track" - Optional.
Gives a long name for the track
frames=multiz28wayFrames - Optional.
Tells the browser which table to
grab the gene frames from.
This is usually associated with
an N-way alignment where the name ends in the string
mafDot=on - Optional.
Use dots instead of bases when bases are identical
visibility=dense|pack|full - Optional.
Sets the default visibility mode for this track.
speciesOrder="hg18 panTro2" - Optional.
White-space separated list specifying the order in which
the sequences in the maf should be displayed.
The second line of a custom MAF track must be a header
line as described below.
Header Line
The first line of a .maf file begins with ##maf.
This word is followed by white-space-separated
variable=value pairs.
There should be no white
space surrounding the &=&.
##maf version=1 scoring=tba.v8
The currently defined variables are:
version - Required.
Currently set to one.
scoring - Optional. A name for the scoring
scheme used for the alignments.
The current scoring schemes are:
bit - roughly corresponds to blast bit
values (roughly 2 points per
aligning base minus penalties for
mismatches and inserts).
blastz - blastz scoring scheme -- roughly
100 points per aligning base.
probability - some score normalized
between 0 and 1.
program - Optional. Name of the program
generating the alignment.
Undefined variables are ignored by the parser.
The header line is usually followed by a comment line (it begins with a #)
that describes the parameters that were used to run the alignment program.
# tba.v8 (((human chimp) baboon) (mouse rat))
Alignment Block Lines (lines starting with 'a' -- parameters for a new alignment block)
a score=23262.0
Each alignment begins with an 'a' line that set
variables for the entire alignment block.
is followed by name=value pairs.
There are no
required name=value pairs.
The currently defined
variables are:
score -- Optional. Floating point score. If
this is present, it is good practice
to also define scoring in the first line.
Positive integer value.
For programs that do multiple pass
alignments such as blastz, this shows
which pass this alignment came from.
Typically, pass 1 will find the
strongest alignments genome-wide, and
pass 2 will find weaker alignments
between two first-pass alignments.
Lines starting with 's' -- a sequence within an alignment block
s hg16.chr7
gcagctgaaaaca
s panTro1.chr6
gcagctgaaaaca
4622798 gcagctgaaaaca
s mm4.chr6
ACAGCTGAAAATA
The 's' lines together with the 'a' lines define a
multiple alignment.
The 's' lines have the
following fields which are defined by position
rather than name=value pairs.
src -- The name of one of the source sequences
for the alignment.
For sequences that
are resident in a browser assembly, the
form 'database.chromosome' allows
automatic creation of links to other
assemblies.
Non-browser sequences are
typically reference by the species name
start -- The start of the aligning region in the
source sequence. This is a
zero-based number. If the strand field
is '-' then this is the start
relative to the reverse-complemented
source sequence (see
size -- The size of the aligning region in the
source sequence.
This number is equal
to the number of non-dash characters in
the alignment text field below.
strand -- Either '+' or '-'.
If '-', then the
alignment is to the
reverse-complemented source.
srcSize -- The size of the entire source sequence,
not just the parts involved in the alignment.
text -- The nucleotides (or amino acids) in
the alignment and any insertions
(dashes) as well.
Lines starting with 'i' -- information about what's
happening before and after this block in the aligning
s hg16.chr7
gcagctgaaaaca
s panTro1.chr6
gcagctgaaaaca
i panTro1.chr6 N 0 C 0
4622798 gcagctgaaaaca
I 234 n 19
The 'i' lines contain information about the context of the
sequence lines immediately preceeding them. The following
fields are defined by position rather than name=value pairs:
src -- The name of the source sequence for the
alignment. Should be the same as the 's' line immediately
above this line.
leftStatus -- A character that specifies the
relationship between the sequence in this block and the
sequence that appears in the previous block.
leftCount -- Usually the number of bases in the aligning
species between the start of this alignment and the end of
the previous one.
rightStatus -- A character that specifies the
relationship between the sequence in this block and the
sequence that appears in the subsequent block.
rightCount -- Usually the number of bases in the
aligning species between the end of this alignment and the
start of the next one.
The status characters can be one of the following values:
C -- the sequence before or after is contiguous with
this block.
I -- there are bases between the bases in this block
and the one before or after it.
N -- this is the first sequence from this src chrom or
n -- this is the first sequence from this src chrom or
scaffold but it is bridged by another alignment from a
different chrom or scaffold.
M -- there is missing data before or after this block
(Ns in the sequence).
T -- the sequence in this block has been used before
in a previous block (likely a tandem duplication)
Lines starting with 'e' -- information about empty parts
of the alignment block
s hg16.chr7
gcagctgaaaaca
e mm4.chr6
The 'e' lines indicate that there isn't aligning DNA for a
species but that the current block is bridged by a chain
that connects blocks before and after this block. The
following fields are defined by position rather than
name=value pairs.
src -- The name of one of the source sequences for the
alignment.
start -- The start of the non-aligning region in the
source sequence. This is a zero-based number. If the
strand field is '-' then this is the start relative to
the reverse-complemented source sequence (see
size -- The size in base pairs of the non-aligning
region in the source sequence.
strand -- Either '+' or '-'. If '-', then the
alignment is to the reverse-complemented source.
srcSize -- The size of the entire source sequence,
not just the parts involved in the alignment.
alignment and any insertions (dashes) as well.
status -- A character that specifies the
relationship between the non-aligning sequence in this
block and the sequence that appears in the previous and
subsequent blocks.
The status character can be one of the following values:
C -- the sequence before and after is contiguous
implying that this region was either deleted in the source
or inserted in the reference sequence. The browser draws a
single line or a '-' in base mode in these blocks.
I -- there are non-aligning bases in the source species
between chained alignment blocks before and after this
block. The browser shows a double line or '=' in base mode.
M -- there are non-aligning bases in the source and
more than 90% of them are Ns in the source. The browser
shows a pale yellow bar.
n -- there are non-aligning bases in the source and the
next aligning block starts in a new chromosome or scaffold
that is bridged by a chain between still other blocks. The
browser shows either a single line or a double line based
on how many bases are in the gap between the bridging
alignments.
Lines starting with 'q' -- information about the quality
of each aligned base for the species
s hg18.chr1
32741 26 +
TTTTTGAAAAACAAACAACAAGTTGG
s panTro2.chrUn
TTTTTGAAAAACAAACAACAAGTTGG
q panTro2.chrUn
s dasNov1.scaffold_179265
4584 TT----------AAGCA---------
q dasNov1.scaffold_179265
99----------32239---------
The 'q' lines contain a compressed version of the actual
raw quality data, representing the quality of each
aligned base for the species with a single character of 0-9
or F. The following fields are defined by position rather
than name=value pairs:
src -- The name of the source sequence for the
alignment. Should be the same as the 's' line immediately
preceding this line.
value -- A MAF quality value corresponding to
the aligning nucleotide acid in the preceding
Insertions (dashes) in the preceding 's' line
are represented by dashes in the 'q' line as well.
The quality value can be 'F' (finished
sequence) or a number derived from the actual quality
scores (which range from 0-97) or the manually assigned
score of 98. These numeric values are calculated as:
MAF quality value = min( floor(actual quality value/5), 9 )
This results in the following mapping:
MAF quality value
Raw quality score range
Quality level
Manually assigned
A Simple Example
Here is a simple example of a three alignment
blocks derived from five starting sequences.
The first track line is necessary for custom
tracks, but should be removed otherwise.
Repeats are shown as lowercase, and each block may
have a subset of the input sequences.
sequence columns and rows must contain at least one nucleotide
(no columns or rows that contain only insertions).
track name=euArc visibility=pack
##maf version=1 scoring=tba.v8
# tba.v8 (((human chimp) baboon) (mouse rat))
a score=23262.0
s hg18.chr7
AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
s panTro1.chr6
AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
4622798 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG
s mm4.chr6
-AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG
s rn3.chr4
-AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG
a score=5062.0
s hg18.chr7
s panTro1.chr6
4622798 TAAAGA
s mm4.chr6
s rn3.chr4
a score=6636.0
s hg18.chr7
gcagctgaaaaca
s panTro1.chr6
gcagctgaaaaca
4622798 gcagctgaaaaca
s mm4.chr6
ACAGCTGAAAATA
& BAM format
BAM is the compressed binary version of the
a compact and index-able representation of nucleotide sequence alignments.
work with SAM/BAM.
For custom track display, the main advantage of indexed BAM over PSL
and other human-readable alignment formats is that only the portions
of the files needed to display a particular region are transferred to
This makes it possible to display alignments from files that
are so large that the connection to UCSC would time out when
attempting to upload the whole file to UCSC.
Both the BAM file and its associated index file remain on your
web-accessible server (http or ftp), not on the UCSC server.
UCSC temporarily caches the accessed portions of the files to speed up
interactive display.
for more information
about BAM custom tracks.
& WIG format
Wiggle format (WIG) allows the display of continuous-valued data in a track
format. Click
information.
& bigWig format
The bigWig format is for display of dense, continuous data that will be
displayed in the Genome Browser as a graph.
BigWig files are
created initially from
(wig) type
files, using the program wigToBigWig.
Alternatively, bigWig
files can be created from
files, using the program bedGraphToBigWig.
In either case, the resulting bigWig files are
in an indexed binary format.
The main advantage of the bigWig files
is that only the portions of the files needed to display a particular
region are transferred to UCSC, so for large data sets bigWig is
considerably faster than regular wiggle files.
The bigWig file remains on your web accessible server (http,
https, or ftp), not on the UCSC server. Only the portion that is needed
for the chromosomal position you are currently viewing is locally cached as a
&sparse file&.
for more information
on the bigWig format.
& Microarray format
The datasets for the built-in microarray tracks in the Genome Browser are stored
in BED15 format, an extension of
format that includes
three additional fields: expCount, expIds, and expScores.
To display correctly in the Genome Browser, microarray tracks
require the setting of several attributes in the trackDb file associated with
the track's genome assembly. Each microarray track set must also have an
associated microarrayGroups.ra configuration file that contains additional
information about the data in each of the arrays.
User-created microarray custom tracks are similar in format to BED
custom tracks with the addition of three required track line parameters in the
header--expNames, expScale, and expStep--that mimic the trackDb and
microarrayGroups.ra settings of built-in microarray tracks.
For a complete description of the microarray track format and an explanation
of how to construct a microarray custom track, see the
& .2bit format
A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a compact
randomly-accessible format. The file contains masking information as well
as the DNA itself.
The file begins with a 16-byte header containing the
following fields:
signature - the number 0x1A412743 in the architecture of the machine that
created the file
version - zero for now. Readers should abort if they see a version number
higher than 0.
sequenceCount - the number of sequences in the file.
reserved - always zero for now
All fields are 32 bits unless noted. If the signature value is not as given,
the reader program should byte-swap the signature and check if the swapped
version matches. If so, all multiple-byte entities in the file will have to be
byte-swapped. This enables these binary files to be used unchanged on
different architectures.
The header is followed by a file index, which contains one entry for
each sequence. Each index entry contains three fields:
nameSize - a byte containing the length of the name field
name - the sequence name itself, of variable length depending on nameSize
offset - the 32-bit offset of the sequence data relative to the start of the
The index is followed by the sequence records, which contain nine fields:
dnaSize - number of bases of DNA in the sequence
nBlockCount - the number of blocks of Ns in the file (representing unknown
nBlockStarts - an array of length nBlockCount of 32 bit integers
indicating the starting position of a block of Ns
nBlockSizes - an array of length nBlockCount of 32 bit integers
indicating the length of a block of Ns
maskBlockCount - the number of masked (lower-case) blocks
maskBlockStarts - an array of length maskBlockCount of 32 bit integers
indicating the starting position of a masked block
maskBlockSizes - an array of length maskBlockCount of 32 bit integers
indicating the length of a masked block
reserved - always zero for now
packedDna - the DNA packed to two bits per base, represented as so:
T - 00, C - 01, A - 10, G - 11.
The first base is in the most significant
2- the last base is in the least significant 2 bits. For example, the
sequence TCAG is represented as .
For a complete definition of all fields in the twoBit format, see
description in the source code.
& .nib format
The .nib format pre-dates the .2bit format and is less compact. It
describes a DNA sequence by packing two bases into each byte.
Each .nib file contains only a single sequence.
The file begins with a 32-bit
signature that is 0x6BE93D3A in the architecture of the machine that created
the file (or possibly a byte-swapped version of the same number on another
machine). This is followed by a 32-bit number in the same format that describes
the number of bases in the file. Next, the bases themselves are listed, packed
two bases to the byte. The first base is packed in the high-order 4 bits
(nibble); the second base is packed in the low-order four bits:
byte = (base1<<4) + base2
The numerical representations for the bases are:
4 - N (unknown)
The most significant bit in a nibble is set if the base is masked.
& GenePred table format
genePred is a table format commonly used for gene prediction tracks in the
Genome Browser. Variations of the genePred format are listed below.
If you would like to obtain browser data in GFF (GTF) format, please refer to
on the Wiki.
Gene Predictions
The following definition is used for gene prediction tables. In
alternative-splicing situations, each transcript has a row in this table.
table genePred
"A gene prediction."
"Name of gene"
"Chromosome name"
"+ or - for strand"
"Transcription start position"
"Transcription end position"
"Coding region start"
"Coding region end"
"Number of exons"
uint[exonCount] exonS "Exon start positions"
uint[exonCount] exonE
"Exon end positions"
Gene Predictions (Extended)
The following definition is used for extended gene prediction tables. In
alternative-splicing situations, each transcript has a row in this table.
The refGene table is an example of the genePredExt format.
table genePredExt
"A gene prediction with some additional info."
"Name of gene (usually transcript_id from GTF)"
"Chromosome name"
"+ or - for strand"
"Transcription start position"
"Transcription end position"
"Coding region start"
"Coding region end"
uint exonC
"Number of exons"
uint[exonCount] exonS "Exon start positions"
uint[exonCount] exonE
"Exon end positions"
"Unique identifier"
string name2;
"Alternate name (e.g. gene_id from GTF)"
string cdsStartS
"enum('none','unk','incmpl','cmpl')"
string cdsEndS
"enum('none','unk','incmpl','cmpl')"
lstring exonF
"Exon frame offsets {0,1,2}"
Gene Predictions and RefSeq Genes with Gene Names
A version of genePred that associates the gene name with the gene prediction
information. In alternative-splicing situations, each transcript has a row in
this table.
table refFlat
"A gene prediction with additional geneName field."
"Name of gene as it appears in Genome Browser."
"Name of gene"
"Chromosome name"
"+ or - for strand"
"Transcription start position"
"Transcription end position"
"Coding region start"
"Coding region end"
"Number of exons"
uint[exonCount] exonS "Exon start positions"
uint[exonCount] exonE
"Exon end positions"
& bigGenePred table format
bigGenePred is a table format commonly used for gene prediction tracks in the
Genome Browser. bigGenePred format is a superset of the
text-based format supported using
format, so it can be efficiently
accessed over a network.
for more information
on the bigGenePred format.
& Personal Genome SNP format
This format is for displaying SNPs from personal genomes.
It is the same as
is used for the Genome Variants and Population Variants tracks.
chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random)
or scaffold (e.g. scaffold10671).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99.
name - The allele or alleles, consisting of one or more A, C, T,
or G, optionally followed by one or more '/' and another allele (there can
be more than 2 alleles). A '-'
can be used in place of a base to denote an i if the
position given is zero bases wide, it is an insertion. The alleles are
expected to be for the plus strand.
alleleCount - The number of alleles listed in the name field.
alleleFreq - A comma-separated list of the frequency of each
allele, given in the same order as the name field.
If unknown, a list of
zeroes (matching the alleleCount) should be used.
alleleScores - A comma-separated list of the quality score of
each allele, given in the same order as the name field.
If unknown, a list
of zeroes (matching the alleleCount) should be used.
In the Genome Browser, when viewing the forward strand of the reference genome
(the normal case), the displayed alleles are relative to the forward strand.
When viewing the reverse strand of the reference genome (via the &<--&
or &reverse& button), the displayed alleles are reverse-complemented
to match the reverse strand. If the allele frequencies are given, the coloring
of the box will reflect the frequency for each allele.
The details pages for this track type will automatically compute amino acid
changes for coding SNPs as well as give a chart of amino acid properties if
there is a non-synonymous change. (The Sift and PolyPhen predictions that are
in some of the Genome Variants subtracks are not available.)
Here is an example of an annotation track in Personal Genome SNP format. The
first SNP using a '-' the second is a deletion. The last 4
SNPs are in a coding region.
track type=pgSnp visibility=3 db=hg19 name="pgSnp" description="Personal Genome SNP example"
browser position chr21:12937
chr21 12008 T/G 2 21,70 90,70
chr21 12032 T/G/A 3 9,60,7 80,80,30
chr21 12035 -/CGG 2 20,80 0,0
chr21 12093 -/CTCGG 2 30,70 0,0
chr21 12278 T 1 15 90
chr21 12772 A 1 36 80
chr21 12828 A/T 2 15,5 0,0
chr21 12880 C 1 0 0
12916 - 1 0 0
& VCF format
is a flexible and extendable
format for variation data such as single nucleotide variants,
insertions/deletions, copy number variants and structural variants.
When a VCF file is compressed and indexed using
, and made web-accesible,
the Genome Browser can fetch only the portions of the file necessary
to display items in the viewed region.
This makes it possible to display alignments from files that
are so large that the connection to UCSC would time out when
attempting to upload the whole file to UCSC.
Both the compressed VCF file and its tabix index file remain on your
web-accessible server (http or ftp), not on the UCSC server.
UCSC temporarily caches the accessed portions of the files to speed up
interactive display.
page for more information about VCF custom tracks.
& ENCODE RNA elements: BED6 + 3 scores format
chrom - Name of the chromosome (or contig, scaffold, etc.).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99.
name - Name given to a region (preferably unique).
Use '.' if no name is assigned.
score - Indicates how dark the peak will be displayed in the
browser (0-1000). If all scores were '0' when the data were submitted to the DCC, the DCC assigned scores 1-1000 based on signal value. Ideally the average signalValue per base spread is between 100-1000.
strand - +/- to denote strand or orientation (whenever
applicable). Use '.' if no orientation is assigned.
level - Expression level such as RPKM or FPKM.
signif - Statistical significance such as IDR.
score2 - Additional measurement/count e.g. number of reads.
& ENCODE narrowPeak: Narrow (or Point-Source) Peaks format
This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.
chrom - Name of the chromosome (or contig, scaffold, etc.).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99.
name - Name given to a region (preferably unique).
Use '.' if no name is assigned.
score - Indicates how dark the peak will be displayed in the
browser (0-1000). If all scores were '0' when the data were submitted to the DCC, the DCC assigned scores 1-1000 based on signal value. Ideally the average signalValue per base spread is between 100-1000.
strand - +/- to denote strand or orientation (whenever
applicable). Use '.' if no orientation is assigned.
signalValue - Measurement of overall (usually, average)
enrichment for the region.
pValue - Measurement of statistical significance (-log10).
Use -1 if no pValue is assigned.
qValue - Measurement of statistical significance using
false discovery rate (-log10). Use -1 if no qValue is assigned.
peak - Point-source
0-based offset
from chromStart. Use -1 if no point-source called.
Here is an example of narrowPeak format:
track type=narrowPeak visibility=3 db=hg19 name="nPk" description="ENCODE narrowPeak Example"
browser position chr1:5000
& ENCODE broadPeak: Broad Peaks (or Regions) format
This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format.
chrom - Name of the chromosome (or contig, scaffold, etc.).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99. If all scores were '0' when the data were submitted to the DCC, the DCC assigned scores 1-1000 based on signal value. Ideally the average signalValue per base spread is between 100-1000.
name - Name given to a region (preferably unique).
Use '.' if no name is assigned.
score - Indicates how dark the peak will be displayed in the
browser (0-1000).
strand - +/- to denote strand or orientation (whenever
applicable). Use '.' if no orientation is assigned.
signalValue - Measurement of overall (usually, average)
enrichment for the region.
pValue - Measurement of statistical significance (-log10).
Use -1 if no pValue is assigned.
qValue - Measurement of statistical significance using
false discovery rate (-log10). Use -1 if no qValue is assigned.
Here is an example of broadPeak format:
track type=broadPeak visibility=3 db=hg19 name="bPk" description="ENCODE broadPeak Example"
browser position chr1:700
& ENCODE gappedPeak: Gapped Peaks (or Regions) format
This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data where the regions may be spliced or incorporate gaps in the genomic sequence. It is a BED12+3 format.
chrom - Name of the chromosome (or contig, scaffold, etc.).
chromStart - The starting position of the feature in the
chromosome or scaffold. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the
chromosome or scaffold. The chromEnd base is not included in the
display of the feature. For example, the first 100 bases of a
chromosome are defined as chromStart=0, chromEnd=100, and span
the bases numbered 0-99.
name - Name given to a region (preferably unique).
Use '.' if no name is assigned.
score - Indicates how dark the peak will be displayed in the
browser (0-1000). If all scores were '0' when the data were submitted to the DCC, the DCC assigned scores 1-1000 based on signal value. Ideally the average signalValue per base spread is between 100-1000.
strand - +/- to denote strand or orientation (whenever
applicable). Use '.' if no orientation is assigned.
thickStart - The starting position at which the feature is drawn thickly.
Not used in gappedPeak type, set to 0.
thickEnd - The ending position at which the feature is drawn thickly.
Not used in gappedPeak type, set to 0.
itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0).
Not used in gappedPeak type, set to 0.
blockCount - The number of blocks (exons) in the BED line.
blockSizes - A comma-separated list of the block sizes. The number of items
in this list should correspond to blockCount.
blockStarts - A comma-separated list of block starts. The first value must be 0
and all of the blockStart positions should be calculated relative to
chromStart. The number of items in this list should correspond to blockCount.
signalValue - Measurement of overall (usually, average)
enrichment for the region.
pValue - Measurement of statistical significance (-log10).
Use -1 if no pValue is assigned.
qValue - Measurement of statistical significance using
false discovery rate (-log10). Use -1 if no qValue is assigned.
Here is an example of gappedPeak format:
track name=gappedPeakExample type=gappedPeak
chr1 600 Anon_peak_1 55 . 0 0 0 2 400,100 0,500 4.55 5.52807
& ENCODE tagAlign: BED3+3 format (historical)
tagAlign was used with hg18, but is no longer in use with hg19.
Tag Alignment provided genomic mapping of short sequence tags.
It is a BED3+3 format.
chrom - Name of the chromosome.
chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
sequence - Sequence of this read.
score - Indicates uniqueness or quality (preferably 1000/alignmentCount).
strand - Orientation of this read (+ or -).
Here is an example of tagAlign format:
chrX 3409 AGAAGGAAAATGATGTGAAGACATA 1000 +
chrX 3412 TCTTATGTCTTCACATCATTTTCCT 500
& ENCODE pairedTagAlign: BED6+2 format (historical)
pairedTagAlign was used with hg18, but is no longer in use with hg19.
Tag Alignment Format for Paired Reads was used to provide genomic mapping of paired-read short sequence tags. It is a BED6+2 format.
chrom - Name of the chromosome.
chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
name - Identifier of paired-read.
score - Indicates uniqueness or quality (preferably 1000/alignment-count).
strand - Orientation of this read (+ or -).
seq1 - Sequence of first read.
seq2 - Sequence of second read.
ENCODE peptideMapping: BED6+4 format
PeptideMapping. The peptide mapping format was used
to provide genomic mapping
of proteogenomic mappings of peptides to the genome, with information
that is appropriate for assessing the confidence of the mapping.&
chrom - Name of the chromosome.
chromStart - The starting position of the feature
in the chromosome. The first base in a chromosome is numbered 0.
- The ending position of the feature in the chromosome or scaffold. The
chromEnd base is not included in the display of the feature. For
example, the first 100 bases of a chromosome are defined as
chromStart=0, chromEnd=100, and span the bases numbered 0-99.
name - The peptide sequence.
score - Indicates uniqueness or quality
(preferably 1000/alignment-count).
strand - Orientation of this read (+ or -).
rawScore - Raw score for this hit, as estimated through HMM analysis.
spectrumId - Non-unique identifier for the spectrum file
peptideRank - Rank of this hit, for peptides with multiple genomic hits>
peptideRepeatCount - Indicates how many times this same hit was observed
& Fasta Format
& FastQ Format