Hi forum,
I suspect that my cufflinks denovo gene model set has many gene models antisense to known transcripts.When this model was use with featurecounts to count hits, I lose reads to many known genes and the unassigned _ambiguous class of reads go up, with unstranded libraries, but not stranded libraries. has any one tried to remove such artifactual gene models?
Thanks!
I suspect that my cufflinks denovo gene model set has many gene models antisense to known transcripts.When this model was use with featurecounts to count hits, I lose reads to many known genes and the unassigned _ambiguous class of reads go up, with unstranded libraries, but not stranded libraries. has any one tried to remove such artifactual gene models?
Thanks!