File Formats

Introduction

IGB supports multiple file formats in both compressed and uncompresed formats. See the links below for information about each of these.

Note that for IGB to recognize a file, the file name must end with one of the supported file format extensions, listed below.

File Types Summary

Type	Extension	Description
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). Supported in IGB 6.3.
BAR	.bar	Binary graph format developed by http://affymetrix.com Affymetrix.
BED	.bed	A tabular format developed for use with the UCSC genome browser. The specifications is available here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
BGR	.bgr	Binary graph format.
Binary Files	.bps, .bgn, .brs, .bsnp, .brpt, .bp1	Binary annotation formats developed specifically for IGB by Affymetrix. These are generally not documented.
BNIB	.bnib	A binary format for sequence data developed for IGB by Affymetrix to speed up loading sequence data over the network.
CHP	.chp	Signal values and presence calls for probesets on Affymetrix microarrays. There are multiple sub-formats, identifiable from the file contents. These files are created by various Affymetrix programs.
CN_SEGMENTS	.cn_segments	Output from Affymetrix Genotyping Console representing a summary of all chromosomal region exhibiting copy number change.
Copy Number Analysis	.cnt	The Affymetrix CNT file format is a tabular format representing output from the Affymetrix CNAT program.
Cytoband	.cyt	A text format for cytoband data to represent cytoBand.txt files from the UCSC genome browser.
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 for associating arbitrary numbers of scores with genomic intervals. The extension ".egr" is preferred. The other extensions are kept for backwards compatibility.
FASTA	.fa, .fasta	Sequence data in a simple ASCII format. See here . Recommended only for short sequences. Otherwise, use 2Bit (see below) or follow these instructions to convert to the ".bnib" format. Note: IGB does not support the use of the Control-A character in the header lines.
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.
PSL	.psl, .psl3, .link.psl	PSL is a tabular format used for representing alignments in UCSC's BLAT tool.
SAM	.sam	The SAM format is not directly supported. Please convert to the binary BAM format via SAMtools. Be sure to index your file as well.
Scored Intervals	.sin, .egr, .egr.txt	See EGR .
Scored Map	.map	An outdated format, replaced now by EGR files.
SGR	.sgr	Tab-delimited graph format.
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.
2Bit	.2bit	2Bit is a compact format for DNA sequences developed by UCSC. Supported in IGB 6.3. See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for more information about it.

File Formats

Introduction

File Types Summary

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