Closed plmsuper8 closed 6 years ago
Dear @plmsuper8 ,
did you specify the BAM files via -B file1 file 1 file 3
? The easiest way would normally to have 3 files, e.g. mate1.txt, mate2.txt and bam_files.txt and have the full path to each of the files in these.
Afterwards, you may specify -mt1 @mate1.txt -mt2 @mate2.txt -B @bam_files.txt
to let DCC know about the files.
Cheers Tobias
Hi @tjakobi,
actually I tried, my command line is as below (the DCC_merge.bamlist contains all .mate1.Aligned, .mate2.Aligned and *Aligned BAMs). But it didn't work.
DCC @DCC_SAMPLES.samplesheet -T 24 -O ./ \ -Pi --filter -R ${IMASK} \ -mt1 @DCC_MATE1.samplesheet -mt2 @/DCC_MATE2.samplesheet \ -B @DCC_merge.bamlist \ -D -G -ss \ -an ${IGTF} \ -Nr 2 5 \ --refseq ${IGENOME}
Dear @plmsuper8,
I think the problem is that you contained all BAMs in the DCC_merge.bamlist
. The file should only contain the non-mate BAM files, i.e. all files should have the same number of lines.
Cheers, Tobias
Hi Tjakobi,
Thanks for your help. it works nicely now.
Best
Hi @tjakobi , I got a problem how to provide all 3 Aligned.bam files to -B list when mapping mate separately ? It kept warning "BAM file list is shorter than mate list". However, if let DCC guess which bam to use, it would only pick *.mate1.Aligned.sortedByCoord.out.bam, which seems incorrect?
Or may I just use BAMs from paired-end alignment? Thx.