Entering edit mode
4.6 years ago
ino
•
0
My understanding is that there are no counting programs using GFF3 files instead of GTF as references.
Is it possible that I can modify the source code of htseq-count or featurecounts and make the modified program public without copyright violation?
You could make a Simplified Annotation Format (SAF) file from your GFF3 and use it with
featureCounts
. Much easier to do than modify source code. Here is an example fromfeatureCounts
manual.Don't modify complex source codes, this will only run you into trouble as you are not aware of the internals of the code. Make it simple, either by creating SAF as genomax recommends or by transforming the gff3 to gtf Convertion Of Gff3 To Gtf