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,
Ren??
-- output of sessionInfo():
--
Sent via the guest posting facility at bioconductor.org.
Dear Ren?,
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, Ren? B?ttcher [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,
> Ren?
>
> -- output of sessionInfo():
>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
