Bamcmp is a tool that allows for an accurate identification of the contaminating host reads when analyzing DNA-Seq and RNA-Seq data from patient-derived xenograft and circulating tumor cell–derived explant models.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=8g [user@cn3316 ~]$ module load bamcmpGet sample input data:
[user@cn3316 ~]$ ln -s $BAMCMP_DATA/SRR4254643_human.bam [user@cn3316 ~]$ ln -s $BAMCMP_DATA/SRR4254643_mouse.bamRun the program:
[user@cn3316 ~]$ bamcmp -n -1 SRR4254643_human.bam -2 SRR4254643_mouse.bam -A SRR4254643_humanBetter.bam -B SRR4254643_mouseBetter.bam -C SRR4254643_humanLoss.bam -D SRR4254643_mouseLoss.bamEnd the interactive session:
[user@cnR3316 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. bamcmp.sh). For example:
#!/bin/bash module load bamcmp cp $BAMCMP_DATA/* . bamcmp -n -1 SRR4254643_human.bam -2 SRR4254643_mouse.bam -A SRR4254643_humanBetter.bam -B SRR4254643_mouseBetter.bam -C SRR4254643_humanLoss.bam -D SRR4254643_mouseLoss.bam
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] bamcmp.sh