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Problem with Cuffcompare to integrate different annotation sources
Hi bioinformatics community!
I have a problem with cuffcompare.
I have different gtf files and I want to integrate them to create a new annotation.
This goal is not impossible and I obtained what I wanted but I have a question: if I have a gtf file with 20360 transcripts and another one of 13677 transcripts why in cuffcompare.tracking file (where I search for the overlap between transcripts) the number of transcripts for q1 (the first gtf file) and q2 (the second gtf file) are lower than in the input file? this difference is around 500/1000 transcripts and I don't know why! It seems that cuffcompare eliminate transcripts in the creation of the new gtf file.
Please help me!!!
I have a problem with cuffcompare.
I have different gtf files and I want to integrate them to create a new annotation.
This goal is not impossible and I obtained what I wanted but I have a question: if I have a gtf file with 20360 transcripts and another one of 13677 transcripts why in cuffcompare.tracking file (where I search for the overlap between transcripts) the number of transcripts for q1 (the first gtf file) and q2 (the second gtf file) are lower than in the input file? this difference is around 500/1000 transcripts and I don't know why! It seems that cuffcompare eliminate transcripts in the creation of the new gtf file.
Please help me!!!
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