[BioC] bam files in sub-directories

[René Böttcher]

Dear Nicolas,

Thank you very much indeed, I did not see that option before, but it 
works nicely if I use pattern="sorted_reads\\.bam$".

Cheers,
René

> 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
> ---------------------------------------------------------------
>
>
>
>
>
> 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.