bam2hints error in gsnap pipeline
Posted: Fri Nov 20, 2015 12:55 pm
Originally posted in the old forum by Philipp Schiffer on 30.01.2014 - 12:51
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
Wait a moment, calculating maximum block size that needs to be allocated... .. done
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
So, my question is if there is something wrong beforehand, as I did all the sorting, or if one has to do the --nomult and that was just missing from the command?
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
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
Code: Select all
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
Code: Select all
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