NAME¶utrrnaseq - identify UTRs in annotated genes from RNA-Seq data
DESCRIPTION¶utrrnaseq is a tool for identifying UTRs of annotated genes on the basis of RNA-Seq data. Starting from known start/stop codons of genes, coverage with RNA-Seq data in potential UTRs is monitored for a drastic drop, and such points are defined as ends of UTRs. Spliced alignments are incorported as introns into UTRs. Drops in coverage due to repeat masking are not reported as UTR endpoints. Only UTR models with evidence from RNA-Seq coverage are reported.
Mandatory parameters¶--in-scaffold-file, -G
Optional arguments¶--in-repeat-file, -R