[BioC] Using easyRNASeq package: question about BAM/BAI and links to them

Martin Morgan mtmorgan at fhcrc.org
Tue Nov 26 19:16:39 CET 2013

On 11/26/2013 10:10 AM, Martin Morgan wrote:
> On 11/26/2013 09:36 AM, Sylvain Foisy Ph. D. wrote:
>> Hi,
>> On 2013-11-26, at 11:55 AM, Nicolas Delhomme wrote:
>>> 1) Is there any possibility that you have circular symlinks, or symlink
>>> chains? I’m not sure how gracefully R would do with symlink chains.
>> Nope, I checked for that.
>>> 2) Are there no permission issues on the bam/bai files or a subset of them?
>> Nope take 2: both locations are own by me with full r+w permissions
>>> 3) Could it be that the symlink names are too long? That used to create
>>> problem in the distant past on some linux distro, but I have not seen it
>>> occurring in years.
>> I made it work when I am in the original location (a single BAM/BAI combo) and
>> it works so the hypothesis of long paths might be it...  I'll see what I can
>> do to rename my stuff with shorter names.
> my guess would be cross-file-system symlinks. Martin

Also, I'm not sure how easyRNASeq does things, but it might be more natural to 
operate on a character() or BamFileList() created with the original file names 
spanning multiple directories. If there are changes in Rsamtools or elsewhere 
that can be made to facilitate that please let me know.


>> Thanks for the time
>> Sylvain
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