[BioC] bam files in sub-directories

[Nicolas Delhomme]

Dear René,

Adding the option recursive=TRUE to your easyRNASeq function call should do just that. 

Let me know if it does not, in which case please post as well your sessionInfo() and easyRNASeq function call.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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On 31 Oct 2012, at 11:05, René Böttcher [guest] wrote:

> 
> 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.