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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.
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| Third-party IGB Apps may support opening files with additional formats. |
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Supported file formats
Type | Extension | Description |
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Affymetrix XML | .axml | A mostly-obsolete XML format used internally at Affymetrix. |
BAM | .bam | A binary indexed version of the SAM format used for displaying alignment data. See SAMtools for more details. |
file unless the location is indicated using the "index" attribute in an IGB Quickload annots.xml configuration file. See About annots.xml. | ||
SAM | .sam | Plain text version of BAM format. Index not required. Recommended for smaller files only. |
BAR | .bar | Binary graph format developed by Affymetrix. Generated from tiling arrays by TAS (Tiling Analysis Software) from Affymerix, cisGenome from Hongkai Ji's research group, and others. |
BED | .bed | A tabular format developed for the UCSC genome browser. IGB supports four, twelve, and fourteen column BED format. In IGB, the thirteenth and fourteenth columns of fourteen-column BED format (also called BED detail format) are interpreted as title and description, respectively. |
BEDGRAPH | .bedgraph | Same as the wiggle format. See below for details. |
BigBED | .bigbed | The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as bed files do. BigBed files are created initially from bed type files, using the program |
BigWIG | .bigwig | Like the bigBED format, this is an indexed form of a WIG file that facilitates incremental data loading and faster loading than the non-indexed, plain text version of the format. See http://genome.ucsc.edu/goldenPath/help/bigWig.html. |
BGR | .bgr | Binary graph format developed by Affymetrix. |
BNIB | .bnib | Binary format for sequence data originally developed for IGB by Affymetrix to speed up loading sequence data over the network. Replaced by 2bit as of IGB 7. |
| CRAM | .cram | A more highly compressed version of the SAM and BAM file formats. Note: Be sure you've indexed your CRAM file (you should have a .crai file as well). The index file must reside in the same folder as the CRAM file unless the location is indicated using the "index" attribute in an IGB Quickload annots.xml configuration file. See About annots.xml. Note: Visualizing CRAM data in IGB requires that you use the EXACT same genome used to align your data. If that genome is not currently available in IGB, see Custom Genomes (Genomes not in IGB). |
Cytoband | .cyt | Text format for representing chromosome band (ideogram) data. Examples are available from the IGBQuickLoad.org site under human genome directories. |
DAS XML files | .das, .dasxml, .das2xml | XML formats returned from DAS servers. See http://www.biodas.org. See DAS/1 specification and DAS/2 specification |
Expression Graphs | .egr, .egr.txt, .sin | EGR is a tabular format representing scored genomic intervals. Files generated from Affymetrix GeneChip Operating Software (GCOS) or ExACT (Exon Array Computational Tool) software. See below for details. |
FASTA | .fa, .fasta, .fna, .fsa, .mpfa, .fas | Sequence data in a simple ASCII format. For larger sequence files (e.g., the human genome) use 2Bit. See Sharing data for a custom genome not already part of IGB QuickLoad. |
GenBank | .gb, .gen | NCBI's file format. IGB has limited support for GenBank files. |
GFF (General Feature Format) | .gff, gtf, .gff3 | General Feature Format. There are several types of GFF file 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. If IGB has difficulty reading your GFF file, make sure the header includes the GFF version, as indicated in the GFF specification documents. |
GR | .gr | Tab-delimited graph format. A simple text format containing two columns of numbers separated by a single space or tab. The first number is the base position; the second number is the score. Because this format does not include chromosome names, we recommend you use .sgr or .wig formats instead. |
PSL | .psl, .psl3, | PSL is a tabular format used for representing alignments in UCSC's BLAT tool. |
| Link.psl | .link.psl | Link.psl represents alignments of Affymetrix target sequences and the location of probe set probes within those sequences. Used to display genomic alignments of Affymetrix probe sets. Ann Loraine wrote some python code for creating link.psl files. See https://bitbucket.org/lorainelab/affyprobesetsforigb and Visualizing probe sets |
PSLX | .pslx | PSLX is an extension to the PSL format that includes the aligned sequence. Aligned sequences are displayed similar to BAM files. |
Scored Intervals | .sin, .egr, .egr.txt | See |
below for details, | ||
Scored Map | .map | An outdated format, replaced now by EGR files. |
SGR | .sgr | Tab-delimited graph format. Sequence graph files that show base coordinate scores. These files are generated by CNAT (the Affymetrix Chromosome Copy Number Analysis Tool software). The format of .sgr text files is: chromosome identification, then two columns of numbers separated by a single space or a tab. The first number is the base position; the second number is the score |
TALLY | .tally | Tally files are created by the bam_tally program (using options -P -B 0), and contain mismatch pileup information. The display is identical to the MisMatch Pileup view mode. The Tally files contain the sequence reference. The plugin will use a tabix index if available. |
USeq | .useq | USeq is a binary indexed format used to display graph and annotation data. Supported in IGB |
9.1.8 and earlier. For more information about it, see: http://useq.sourceforge.net. | ||
| VCF | .vcf | Variant Call Format (VCF) is a flexible and extendable format for variation data such as single nucleotide variants, insertions/deletions, copy number variants and structural variants. More information on the VCF file format can be found here: https://github.com/samtools/hts-specs |
Wiggle | .wig | This is a text format for graphical data designed for the UCSC genome browser. IGB supports all 3 subtypes: BED, variableStep, fixedStep. For more information, see the UCSC Web page describing the format: http://genome.ucsc.edu/goldenPath/help/wiggle.html. Files in wiggle format can use UCSC track lines to specify colors and other properties. |
2Bit | .2bit | 2Bit is a compact format for DNA sequences developed by UCSC. See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for more information about it |
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Files Types Supported Through Plugins
Some file formats can be read after installing the appropriate plug-in. See Plug-ins.
About GFF and its variants
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The GFF3 format is described here http://song.sourceforge.net/gff3-jan04.shtml
About
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bedGraph
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A "wig" file is a data file that bedGraph file associates numerical values (e.g., read coverage) with a region of the genome. For example, here is an excerpt: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.
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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, you'll see this "name" attribute again in the name will appear as the track label.
Partial data loading using tabix indexed files
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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.
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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]*
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