[BioC] easyRNASeq - error reading single chromosome bam

[Nicolas Delhomme]

Hi Francesco,

I'd need more info to help you.

Can you post the header of your bam files and the content of as.list(seqlengths(Hsapiens)).

In the meanwhile can you run easyRNASeq with normalize set to FALSE, no conditions and the outputFormat set to "RNAseq"?

That will give you back the RNAseq object and we can have a look at what is happening in there. 

I get the feeling that it has to do with the exon names being converted into integers (through the use of a factor maybe) but I thought I got that bug squashed already...

Cheers,

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 7 Feb 2012, at 13:37, Lescai, Francesco wrote:

> Hi there,
> I'm preparing a tutorial, therefore I sliced two RNASeq bam files from chromosome one, in order to reduce the file size.
> 
> However, when I count the reads as it follows I have an error.
> thanks,
> Francesco
> 
> 
>> countDataSet <- easyRNASeq(filesDirectory=getwd(),
> +                            organism="HSapiens",
> +                            chr.sizes=as.list(seqlengths(Hsapiens)),
> +                            readLength=100L,
> +                            annotationMethod="biomaRt",
> +                            format="bam",
> +                            count="exons",
> +                            filenames=bamfiles,
> +                            normalize=TRUE,
> +                            outputFormat="DESeq",
> +                            conditions=conditions,
> +                           fitType="local"
> +                           )
> Checking arguments...
> Fetching annotations...
> Summarizing counts...
> Processing SRR349689_1.fastq.novo.new.chr1.bam
> Error in FUN(c("GL000229.1", "GL000200.1", "GL000228.1", "GL000241.1",  :
>  (list) object cannot be coerced to type 'integer'
> 
> I also tried selecting the chromosome with chr.sel=c("1") or chr.sel=c("chr1") but in both cases I get the error
> Make sure that your file is valid, that your 'chr.sel' (if provided) contains valid values; i.e. values as found in the file, not as returned by 'RNAseq'.
> 
> The alignment has been done using the ENSEMBL reference, i.e. with chromosome listed as "1".
> 
> sessionInfo()
> R Under development (unstable) (2012-01-20 r58146)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] GenomicFeatures_1.6.7              AnnotationDbi_1.17.15              easyRNASeq_1.1.5
> [4] ShortRead_1.13.13                  latticeExtra_0.6-19                RColorBrewer_1.0-5
> [7] Rsamtools_1.7.27                   genomeIntervals_1.11.0             intervals_0.13.3
> [10] DESeq_1.7.6                        locfit_1.5-6                       lattice_0.20-0
> [13] akima_0.5-7                        BiocInstaller_1.3.7                Biobase_2.15.3
> [16] edgeR_2.5.9                        limma_3.11.11                      biomaRt_2.11.1
> [19] BSgenome.Hsapiens.UCSC.hg19_1.3.17 BSgenome_1.23.2                    Biostrings_2.23.6
> [22] GenomicRanges_1.7.16               IRanges_1.13.22                    BiocGenerics_0.1.4
> 
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5          RCurl_1.9-5        RSQLite_0.11.1     XML_3.8-0          annotate_1.33.2
> [6] bitops_1.0-4.1     genefilter_1.37.0  geneplotter_1.33.1 grid_2.15.0        hwriter_1.3
> [11] rtracklayer_1.15.7 splines_2.15.0     survival_2.36-10   tools_2.15.0       xtable_1.6-0
> [16] zlibbioc_1.1.1
> 
> 
> ---------------------------------------------------------------------------------
> Francesco Lescai, PhD, EDBT
> Senior Research Associate in Genome Analysis
> University College London
> Faculty of Population Health Sciences
> Dept. Genes, Development & Disease
> ICH - Molecular Medicine Unit, GOSgene team
> 30 Guilford Street
> WC1N 1EH London UK
> 
> email: f.lescai at ucl.ac.uk<mailto:f.lescai at ucl.ac.uk>
> phone: +44.(0)207.905.2274
> [ext: 2274]
> --------------------------------------------------------------------------------
> 
> 
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