[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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