search

dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
36 stars 20 forks source link

Cannot provide mate separate mapping BAMs to -B list #45

Closed plmsuper8 closed 6 years ago

plmsuper8 commented 6 years ago

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.

tjakobi commented 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

plmsuper8 commented 6 years ago

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}

tjakobi commented 6 years ago

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

plmsuper8 commented 6 years ago

Hi Tjakobi,

Thanks for your help. it works nicely now.

Best