Gffread filters and or or converts GFF3 or GTF2 records
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.