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Old 03-08-2016, 12:27 AM   #8
colindaven
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Location: Germany

Join Date: Oct 2008
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A GMAP command which produces GFF3 output might look like this:

~/gmap-2015-07-23/bin/gmap -f gff3_gene -D gmap/ -d mygenome.fasta.gmap -B 5 -t 12 --intronlength=50000 --totallength=1000000 -p 3 --npaths=1 transcripts.fa > transcripts.gff3

This is a nice GFF3 which can be used directly by "bedtools multicov"

If you want to use featureCounts for read counting try using ngsutils to convert from gff3 to gtf.

http://ngsutils.org/modules/gtfutils/
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