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

Sylvain Foisy Ph. D. sylvain.foisy at diploide.net
Tue Nov 26 17:36:51 CET 2013


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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