IGB supports multiple file formats in both compressed and uncompressed formats. See the table below for details and links (when available) to resources describing each format. IGB uses file extensions to recognize file formats, listed below.

Supported file formats

About GFF and its variants

GFF stands for 'general feature format' or 'gene finding format'; it is a tab-delimited file with 9 columns. There are several types of GFF files that use incompatible syntax. The original GFF format is GFF1. A variant called GTF is also used. GFF3 has been proposed to extend on GFF and to constrain the specification more tightly to avoid mutually-incompatible versions of GFF. Some GFF files created by Affymetrix make use of extensions to GFF that are specific to IGB. These are indicated in the file headers by lines beginning with "##IGB-".

IGB can handle most versions of GFF/GTF, but may have difficulty with some rarely-used advanced features. IGB does not read any FASTA data that is included in some GFF3 files. If IGB has difficulty reading your GFF file, make sure that there is a line in the header similar to ##gff-version 2 that identifies the correct format number 1, 2 or 3.

The GFF format is described at http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

The GTF format is described here http://genes.cs.wustl.edu/GTF2.html

The GFF3 format is described here http://song.sourceforge.net/gff3-jan04.shtml

About bedGraph

A bedGraph file associates numerical values (e.g., read coverage) with regions of a genome assembly. Note that the data for an entire genome can reside in a single file. If using this format, you should sort it and index it using tabix for faster and more memory-efficient data loading.

track type=bedGraph name="Pollen RNA-Seq coverage"
chr1	0	3722	0
chr1	3722	3797	1
chr1	3797	5890	0
chr1	5890	5893	4
chr1	5893	5897	5
chr1	5897	5902	6
chr1	5902	5910	7
chr1	5910	5939	8
chr1	5939	5944	9
chr1	5944	5957	10

Note that the top line of the file contains information (meta-data) about the data set, including its name. When you open the file in IGB, the name will appear as the track label.

Partial data loading using tabix indexed files

IGB supports partial data loading of several file types using tabix indexing. Supported file types include SAM, BED, BEDGRAPH, PSL, and PSLX.

Indexed files allow for faster searching and loading. The indexed file and its index (.tbi file) must reside in the same folder either on your local computer or on a server.  More about tabix can be found here.

Sequence File Formats

IGB supports fasta and 2bit formats. Older versions of IGB also support an IGB-specific format called bnib. Newer versions of IGB will probably still open bnib files, but as of IGB 7.0, we are no longer including the bnib format in our testing process.

FASTA files contain sequence data in a simple ASCII format. For details, Google search fasta.

BNIB is an older format developed for IGB that makes it possible to represent sequence data in a very compact format. 2bit, developed at UCSC is also a compact, binary format for representing sequence data, but a number of open source tools are available for working with this format and so for this reason, IGB now uses 2bit instead of bnib.

.egr and .sin Formats

EGR (also known as Scored Interval, .sin, format.files) are TAB-delimited files with a header. They can contain one or more scores associated with named annotations or with named or unnamed genomic regions. They have an optional header section which is a list of tag-value pairs, one per line, in the form: # tag = value Currently the only tags used by the parser are of the form score$i (score name tags are optional). If score name tags are present, then score number $i will be named according to the value of the score$i tag. If any score name tags are missing, default names will be created.

It is recommended that a tag value pair with the genome version, such as #genome_version = H_sapiens_May_2004 , be included to indicate which genome assembly the sequence coordinates are based on. This will ensure that the file is being compared to other annotations from the same assembly.

There are three versions of this format. They can all be described this way, where the parentheses indicate optional elements:(annot_id) ((seqid) min_coord max_coord strand) [score]*

1. seqid is word string [a-zA-Z_0-9]+
2. min_coord is int
3. max_coord is int
4. strand can be '+', '-', or '.' for "unknown"
5. score is float
6. annot_id is word string [a-zA-Z_0-9]+

All lines must have same number of columns. Format 1 has tab-delimited lines with 4 required columns, any additional columns are scores:seqid min_coord max_coord strand [score]* Format 2 has tab-delimited lines with 5 required columns, any additional columns are scores:annot_id seqid min_coord max_coord strand [score]* Format 3 has tab-delimited lines with 1 required column, any additional columns are scores:annot_id [score]* The IGB parser should be able to distinguish between these, based on combination of number of fields, and presence and position of the strand field. For use in IGB, EGR version 3 is dependent on prior loading of annotations with matching ids.

Examples

• Format 1:# genome_version = H_sapiens_Apr_2003

1. score0 = A375
2. score1 = FHS
   gene1 chr22 14433291 14433388 + 140.642 175.816
   gene2 chr22 14433586 14433682 + 52.3838 58.1253
   gene3 chr22 14434054 14434140 + 36.2883 40.7145

• Format 2:# genome_version = H_sapiens_Apr_2003

1. score0 = A375
2. score1 = FHS
   chr22 14433291 14433388 + 140.642 175.816
   chr22 14433586 14433682 + 52.3838 58.1253
   chr22 14434054 14434140 + 36.2883 40.7145

• Format 3:(assumes annotations with the names gene1, gene2, and gene3 are already loaded.)# genome_version = H_sapiens_Apr_2003

1. score0 = A375
2. score1 = FHS
   gene1 140.642 175.816
   gene2 52.3838 58.1253
   gene3 36.2883 40.7145