[BioC] bam files in sub-directories

[René Böttcher [guest]]

Hi,

I wanted to ask whether there is an option within the easyRNASeq method to specify sub-directories containing the bam files I want to analyse. 

My directory structure looks like this

-alignments
  -sample1_mapping/
    -sorted_reads.bam
    -sorted_reads.bam.bai
  -sample2_mapping/
    -sorted_reads.bam
    -sorted_reads.bam.bai
...

So is it possible to run easyRNASeq without throwing all bam files in one directory?
Thus far, the only option I could think of would be to run easyRNASeq for every of my sample folders independently and then merge the resulting count objects somehow.

Any help is greatly appreciated.
Best regards,
René

 -- output of sessionInfo(): 

 

--
Sent via the guest posting facility at bioconductor.org.