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

Nicolas Delhomme nicolas.delhomme at umu.se
Tue Nov 26 20:36:55 CET 2013


On 26 Nov 2013, at 19:16, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> 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.
> 

It does operate on character and you could provide the recursive = TRUE arguments to the easyRNASeq command. BamFileList is implemented in my Git version of easyRNASeq, which I hope to release soon.

Nico

> Martin
> 
>> 
>>> Thanks for the time
>>> 
>>> Sylvain
>>> 
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>> 
>> 
> 
> 
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