[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
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?
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 parallel stats graphics grDevices utils datasets methods
other attached packages:
 easyRNASeq_1.8.2 ShortRead_1.20.0 Rsamtools_1.14.2
 GenomicRanges_1.14.3 DESeq_1.14.0 lattice_0.20-24
 locfit_1.5-9.1 Biostrings_2.30.1 XVector_0.2.0
 IRanges_1.20.6 edgeR_3.4.0 limma_3.18.3
 biomaRt_2.18.0 Biobase_2.22.0 genomeIntervals_1.18.0
 BiocGenerics_0.8.0 intervals_0.14.0
loaded via a namespace (and not attached):
 annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-6
 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0
 grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26
 LSD_2.5 RColorBrewer_1.0-5 RCurl_1.95-4.1
 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2
 survival_2.37-4 XML_3.98-1.1 xtable_1.7-1
> 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:
And I created my symlinks something like this:
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",
> 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:
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 ;-)
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