I am using docker containers to run a pipeline for RNA-seq analysis. Specifically, I am using cufflinks now, to quantitate and annotate the transcripts. I am dealing with 770 .bam files (aligned by TopHat), and running the following code for each one of them:
cufflinks -b hg19.fa -g hg19.refGene.gtf -u [sample.bam]
I would very much like to let cufflinks run across all those samples without the need of manually putting the command for each one of them. And that would also allow for the machine to run non-stop until it's done. So, my question is:
Is there any way to create an iteration procedure/command for that?
PS: I am running the docker image within an interactive shell (arguments
Any help is very much appreciated!