Hi!
I am following the http://bioinf.uni-greifswald.de/bioinf/ ... Aseq.GSNAP manual to incorporate gsnap mapped RNAseq reads to create a hints file.
Following the steps of sorting and filtering I get an error when it finally comes to
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bam2hints --intronsonly --in=B3I_UNclean_shuf.gsnap.Bornheim.Bornheimx.result.ref.ss.f.bam --out=hints-sort.gff
BAM file MUST be sorted by target sequence names when 'intronsonly' and 'mult' options are active
This happens regardless if I do the last filtering step
samtools sort rnaseq.f.bam rnaseq.fs
or not. It does work when I set the
--nomult switch, so
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bam2hints --intronsonly --nomult --in=rnaseq.fs.bam --out=hints.gff.
My guess was that having the mult option would make sense if that puts more power to one specific hint, but then it might just not do anything like that?
Thanks
Philipp