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

Nicolas Delhomme nicolas.delhomme at umu.se
Tue Nov 26 17:55:15 CET 2013


Beats me… 

I’m really hitting in the dark here but:

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. 

2) Are there no permission issues on the bam/bai files or a subset of them?

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.

Nico

---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On 26 Nov 2013, at 17:36, Sylvain Foisy Ph. D. <sylvain.foisy at diploide.net> wrote:

> Hi Nicolas,
> 
> On 2013-11-26, at 11:13 AM, Nicolas Delhomme wrote:
> 
>> Bonsoir Sylvain,
>> 
>> I have never encountered that situation. I’ve tried to reproduce it but to no avail.
> 
> Well, that would not be the first time but usually, I am in your position ;-) Ok, here goes:
> 
>> 1) report your sessionInfo() to make sure you are using R-3.0.2 and easyRNASeq-1.8.2?
> 
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods 
> [8] base     
> 
> other attached packages:
> [1] easyRNASeq_1.8.2       ShortRead_1.20.0       Rsamtools_1.14.2      
> [4] GenomicRanges_1.14.3   DESeq_1.14.0           lattice_0.20-24       
> [7] locfit_1.5-9.1         Biostrings_2.30.1      XVector_0.2.0         
> [10] IRanges_1.20.6         edgeR_3.4.0            limma_3.18.3         
> [13] biomaRt_2.18.0         Biobase_2.22.0         genomeIntervals_1.18.0
> [16] BiocGenerics_0.8.0     intervals_0.14.0      
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.40.0      AnnotationDbi_1.24.0 bitops_1.0-6        
> [4] DBI_0.2-7            genefilter_1.44.0    geneplotter_1.40.0  
> [7] grid_3.0.2           hwriter_1.3          latticeExtra_0.6-26 
> [10] LSD_2.5              RColorBrewer_1.0-5   RCurl_1.95-4.1      
> [13] RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2        
> [16] survival_2.37-4      XML_3.98-1.1         xtable_1.7-1        
> [19] zlibbioc_1.8.0 
> 
> 
>> 2) give me a glance of your symlink structure to see if my mockup recapitulated your case?
> 
> Basically, my BAM/BAI file combos are located in something like this:
> 
> given/location/sampleID/tissue/accepted_hits.bam
> given/location/sampleID/tissue/accepted_hits.bam.bai
> 
> And I created my symlinks something like this:
> 
> another/location/sample_tissue_accepted_nits.bam
> another/location/sample_tissue_accepted_nits.bam.bai
> 
> So that all the symlinks are under a single location instead.
> 
>> 3) can you try to reproduce the following:
>> 
>> Here is what I did to test easyRNASeq on what I guess was your symlink structure:
>> 
>> a) first I created symlinks in my Desktop/tmp dir:
>> 
>> lrwxr-xr-x  1 delhomme  staff  71 Nov 26 17:02 ACACTG.bam -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ACACTG.bam
>> lrwxr-xr-x  1 delhomme  staff  75 Nov 26 17:02 ACACTG.bam.bai -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ACACTG.bam.bai
>> lrwxr-xr-x  1 delhomme  staff  71 Nov 26 17:02 ACTAGC.bam -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ACTAGC.bam
>> lrwxr-xr-x  1 delhomme  staff  75 Nov 26 17:02 ACTAGC.bam.bai -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ACTAGC.bam.bai
>> lrwxr-xr-x  1 delhomme  staff  71 Nov 26 17:02 ATGGCT.bam -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ATGGCT.bam
>> lrwxr-xr-x  1 delhomme  staff  75 Nov 26 17:02 ATGGCT.bam.bai -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/ATGGCT.bam.bai
>> lrwxr-xr-x  1 delhomme  staff  71 Nov 26 17:02 TTGCGA.bam -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/TTGCGA.bam
>> lrwxr-xr-x  1 delhomme  staff  75 Nov 26 17:02 TTGCGA.bam.bai -> /Users/delhomme/Library/R/3.0/library/RnaSeqTutorial/extdata/TTGCGA.bam.bai
>> 
>> pointing to the example data package (RnaSeqTutorial) companion of easyRNASeq.
>> 
>> b) then in R I ran:
>> 
>> counts <- easyRNASeq(filesDirectory="Desktop/tmp",
>>                    pattern="[A,C,T,G]{6}\\.bam$",
>>                    readLength=30L,chr.sel="chr2L",
>>                    organism="Dmelanogaster",
>>                    annotationMethod="rda",
>>                    annotationFile=system.file("data","gAnnot.rda",package="RnaSeqTutorial"),
>>                    count="exons")
>> 
>> 
>> and I got the expected count table.
> 
> Ok, along the suggested lines, I installed the RnaSeqTutorial package and symliked the BAM/BAI files from their location to a ~/test folder and am running this command:
> 
> count.table<-easyRNASeq(filesDirectory="/shares/home/foisys/test",
>                    pattern="[A,C,T,G]{6}\\.bam$",
>                    readLength=30L,chr.sel="chr2L",
>                    organism="Dmelanogaster",
>                    annotationMethod="rda",
>                    annotationFile=system.file("data","gAnnot.rda",package="RnaSeqTutorial"),
>                    count="exons")
> 
> and it is working...
> 
>> 
>> 4) btw, how did you create the links? As far as I remember, Windows does not create symlink in the same way a Unix system does, which is what I tried here. 
> 
> I am 100% Linux ;-)
> 
> Best regards
> 
> Sylvain
> 



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