Question: Can we make a counting program using GFF3 reference files?
0
gravatar for ino
3 months ago by
ino0
ino0 wrote:

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?

ADD COMMENTlink written 3 months ago by ino0
2

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 from featureCounts manual.

GeneID      Chr Start   End Strand
497097      chr1    3204563 3207049 -
497097      chr1    3411783 3411982 -
497097      chr1    3660633 3661579 -
100503874   chr1    3637390 3640590 -
100503874   chr1    3648928 3648985 -
100038431   chr1    3670236 3671869 -
ADD REPLYlink written 3 months ago by genomax74k

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

ADD REPLYlink written 3 months ago by ATpoint26k
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