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By Trapnell C., Pachter L. , Last update 1494698999
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cuffcompare description

Cuffcompare provides classification, reference annotation mapping and various statistics for Cufflinks transfrags. Cuffcompare clusters and tracks transfrags across multiple samples, writing matching transcripts (intron chains) into .tracking, and a GTF file .combined.gtf containing a nonredundant set of transcripts across all input files (with a single representative transfrag chosen for each clique of matching transfrags across samples).

Parent program: cufflinks

Cufflinks is a software for estimation of gene expression levels. It performs reference-guided assembly of aligned RNA-seq reads into a set of transcripts and then evaluates the relative abundances of these transcripts by counting supporting reads. Cufflinks is a part of the Tuxedo protocol for RNA-Seq data processing. It is recommended to use Tophat output RNA-seq read alignment file in SAM or BAM format as input, but Cufflinks can accept SAM or BAM files created by any read mapper.