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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Multiple bam files input #86

Closed KaushikPanda1 closed 5 years ago

KaushikPanda1 commented 5 years ago

Hello,

Is there a way to input multiple bam files for downstream analysis using ShortStack? The program takes multiple input read files (space separated) for aligning, however does not recognize multiple bam files to perform just downstream analysis. I am able to get around the problem by merging the bam files first and using that single merged bam file as input.

Just wondering if I am doing something wrong.

Thanks, Kaushik.

MikeAxtell commented 5 years ago

Hi Kaushik.

Nope, only one bam file. Merging first yourself is the solution if you don't want to let ShortStack also handle the alignments by feeding in multiple read files. Note that the Counts.txt file will contain read counts per locus per read group if the single input BAM file had more than one read-group.

Cheers, Mike

On Fri, Dec 7, 2018 at 4:39 PM Kaushik Panda notifications@github.com wrote:

Hello,

Is there a way to input multiple bam files for downstream analysis using ShortStack? The program takes multiple input read files (space separated) for aligning, however does not recognize multiple bam files to perform just downstream analysis. I am able to get around the problem by merging the bam files first and using that single merged bam file as input.

Just wondering if I am doing something wrong.

Thanks, Kaushik.

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