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.
Note: Be sure you've indexed your BAM file (you should have a .bai file as well). The index file must reside in the same folder as the BAM

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 bedToBigBed. The 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 loaded into IGB, so for large data sets bigBed is considerably faster than regular bed files. See http://genome.ucsc.edu/goldenPath/help/bigBed.html.

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.

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.

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 6.2. For more information about it, see: http://useq.sourceforge.net.

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.