ChIP-Convert Module
Format Converter Tool
Background: ChIP-Converter converts data from BED, GFF, BAM, ELAND or FPS formats to SGA format, which is the internal working format of the ChIP-Seq programs.
BED format Browser Extensible Data has been designed at UCSC for displaying data traks in the genome browser.
GFF format Generic Feature Format is a format for describing genes and other features associated with DNA, RNA and protein sequences.
BAM format Binary Alignment/Map is derived from the SAM format which is a geneirc alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128Mbp) produced by different sequencing platforms.
ELAND format Efficient Large Scale Alignment of Nucleotide Databases is the export format (tab-delimited file, output of ELAND aligner) of the Illumina sequencing data processing pipeline.
FPS format Functional Position Set is a format used by the Signal Search Analysis (SSA) programs for representing a set of DNA or RNA sequences which occur at a constrained distance from a functional site, for instance a transcription initiation site or a transcription factor binding site.
The Converter tool also provides SGA-to-BED, SGA-to-GFF, SGA-to-FPS, BAM-to-BED and BED-to-BAM conversion. File compression at both input and output in gzip format is also supported.
BED format Browser Extensible Data has been designed at UCSC for displaying data traks in the genome browser.
GFF format Generic Feature Format is a format for describing genes and other features associated with DNA, RNA and protein sequences.
BAM format Binary Alignment/Map is derived from the SAM format which is a geneirc alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128Mbp) produced by different sequencing platforms.
ELAND format Efficient Large Scale Alignment of Nucleotide Databases is the export format (tab-delimited file, output of ELAND aligner) of the Illumina sequencing data processing pipeline.
FPS format Functional Position Set is a format used by the Signal Search Analysis (SSA) programs for representing a set of DNA or RNA sequences which occur at a constrained distance from a functional site, for instance a transcription initiation site or a transcription factor binding site.
The Converter tool also provides SGA-to-BED, SGA-to-GFF, SGA-to-FPS, BAM-to-BED and BED-to-BAM conversion. File compression at both input and output in gzip format is also supported.
Last update 7 Mar. 2012
