multiple input bam files

[ccshao]

How could I run QoRTs on multiple bam files in the java command line? It seems only one sample is accepted in the java command line.
Would be possible to make something like following work? or give a file with path of bam files per line?

java -jar QoRTs.jar QC \
        --singleEnded \
        --generatePlots \
        EXAMPLE1.s.bam \
        EXAMPLE.2s.bam \
        $gtf \
        ./EXAMPLE_QoRTs/

Thanks!

[hartleys]

So what would it do? Combine the bam files together? Or do you just want a single command that runs multiple separate samples?

…

On Tue, Jul 31, 2018, 3:43 AM shao ***@***.***> wrote: How could I run QoRTs on multiple bam files in the java command line? It seems only one sample is accepted in the java command line. Would be possible to make something like following work? or give a file with path of bam files per line? java -jar QoRTs.jar QC \ --singleEnded \ --generatePlots \ EXAMPLE1.s.bam \ EXAMPLE.2s.bam \ $gtf \ ./EXAMPLE_QoRTs/ Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#67>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7Mw1ZGxcqKQ4JQkGHT7uyBwJaC1zks5uMAqvgaJpZM4Vnwe3> .

[ccshao]

the latter idea, a single command run all listed samples, or read from files has the bam files