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Old 02-17-2016, 01:48 AM   #3
sbcn
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Location: spain

Join Date: Oct 2012
Posts: 16
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Thanks a lot for your input.

I have now tried gffcompare, but it is actually a lot worse in my case:

gffcompare -r reference.gtf -s reference.fa -C -D -i gtf_list.txt

awk '$3=="transcript"' gffcmp.combined.gtf | wc -l
# 185653

As I understand it, gffcompare creates the union of all the gtf files given as an input, and as I am merging about 60 files, I get a huge final number of transcripts.

I think stringtie --merge is more appropriate in my case as it rather constructs a kind of consensus, so I will try and work on optimizing the parameters, although I would like to make sure not to be too stringent on some of them, and too flexible on others.
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