Hi,

I am trying to use easyRNASeq to create count tables for DESeq analysis. I have about a hundred BAM files with their associated indexes, located in my file system and sorted in folders, on for each provider and in each one folder for each tissue. To not use to much space, I created simlinks from each of these BAM/BAI combo toward a single location so that easyRNASeq can read them all. When I try my command, I get this error:

Error in easyRNASeq(filesDirectory = "/shares/data2/tmp01/inflammgen_temp_transfer/htseq_datastore/RNASeq_datastore/RNASeq_comprehensive_catalog/4.diff_ex_analysis/4.0.link2files/2013_10_29-16_00_07_NCBI_build37.from.2.2.phred_q_trimming_2013_10_24",  :
  Index files (bai) are required. They are missing for the files: blablabla...

But, the files are there :-( I removed the BAI symlinks and cp the real files to the same location and I get the same mistake... Is my idea of symlinking from the source the problem?

Any idea appreciated ;-)

Best regards

Sylvain

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Sylvain Foisy, Ph. D.
Chargé de projet | Project Manager
Bioinformatics
Labo. de génétique et médecine génomique de l'inflammation
Centre de recherche
Institut de cardiologie de Montréal
5000 Bélanger Est
Montréal, Qc  H1T 1C8
CANADA

T: (514) 376-3330 x.2299
F: 514-593-2539
M: sylvain.foisy@inflammgen.org<mailto:sylvain.foisy@inflammgen.org>
W: http://inflammgen.org
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