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, Ren? > 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.