[BioC] bam file in easyRNASeq

[Nicolas Delhomme]

Hi Silav,

You need to give the BAM file as input (filenames="accepted_hits.bam") and not the BAM index file ("accepted_hits.bam.bai"). The bam index file is necessary though, but it's filename is deduced from the BAM file name.

You're using an older version of R/Bioc/easyRNASeq than the currently supported one. You should move R to 2.15.2 with Bioc 2.11 (easyRNASeq 1.4.2). I hadn't seen your comment about the IT before writing that, but you can very probably install that as your own user in your home directory. Can't you really install the latest R dmg package as a user (I haven't tried this myself)?

Here is how I do myself (on Mac too) using the terminal. You might need some system libraries to be installed, but they might be there if IT has R already installed on the system. If not (my case), I'm using macports (http://www.macports.org/) to get the necessary libraries (takes a little while to set up, but it works like a charm now). 

download the latest R from you CRAN mirror
tar -zxf R-2.15.2.tar.gz
mv R-2.15.2 R-2.15.2_SRC
cd R-2.15.2_SRC
./configure --prefix=`pwd`/../R-2.15.2 --enable-R-shlib
make
make check
make pdf
make info
make install
make install-info
make install-pdf

Then R is accessible as R-2.15.2/bin/R. Just adding R-2.15.2/bin to the PATH environment variable makes you using your R whenever you type R on the command line.

HTH,

Nico


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

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 13 Dec 2012, at 07:42, Silav Bremos wrote:

> Hello list
> 
> rnaSeq <- easyRNASeq(filesDirectory=getwd(),
>     filenames="accepted_hits.bam.bai",
>     organism="Dmelanogaster",
>     chr.sizes=as.list(seqlengths(Dmelanogaster)),
>     readLength=36L,
>     annotationMethod="gtf",
>     annotationFile="/myrnaseqB/genes.gtf",
>       format="bam", gapped=TRUE,
>     count="exons",
>     outputFormat="RNAseq")    
> 
> I keep getting this error:
> Checking arguments... 
> Error in easyRNASeq(filesDirectory = getwd(), filenames = "accepted_hits.bam.bai",  : 
>   Index files (bai) are required. They are missing for the files: /myrnaseqB/C2_R2_thout/accepted_hits.bam.bai
>   
> even after 
>> sortBam("accepted_hits.bam","accepted_hits") 
>> indexBam(files="accepted_hits.bam")
>> file.exists("/myrnaseqB/C2_R2_thout/accepted_hits.bam.bai")
> [1] TRUE
> 
> Please help. I will not be able to upgrade or reinstall. IT dept does that on their schedule.
> 
> Silav
> --------------------------------------------------------- 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
>  [1] easyRNASeq_1.2.5       ShortRead_1.14.4       latticeExtra_0.6-24    RColorBrewer_1.0-5    
>  [5] lattice_0.20-10        Rsamtools_1.8.6        DESeq_1.8.3            locfit_1.5-8          
>  [9] BSgenome_1.24.0        GenomicRanges_1.8.13   Biostrings_2.24.1      IRanges_1.14.4        
> [13] edgeR_2.6.12           limma_3.12.3           biomaRt_2.12.0         Biobase_2.16.0        
> [17] genomeIntervals_1.12.0 BiocGenerics_0.2.0     intervals_0.13.3      
> 
> loaded via a namespace (and not attached):
>  [1] annotate_1.34.1      AnnotationDbi_1.18.4 bitops_1.0-4.2       DBI_0.2-5            genefilter_1.38.0   
>  [6] geneplotter_1.34.0   grid_2.15.0          hwriter_1.3          RCurl_1.95-3         RSQLite_0.11.2      
> [11] splines_2.15.0       stats4_2.15.0        survival_2.37-2      tools_2.15.0         XML_3.95-0.1        
> [16] xtable_1.7-0         zlibbioc_1.2.0      
> 	[[alternative HTML version deleted]]
> 
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