Hello,
I am using R-dev, and would like to run QuasR to align a RNA-seq experiment.
Unfortunately, I can't get past the indexing step because somehow BSgenome cannot be accessed by QuasR.
I think this is due because it can be accessed by using "Rnorvegicus" rather than by (the expected)  "BSgenome.Rnorvegicus.UCSC.rn5".

Is this to be changed in QuasR, or the BSgenome?

Thanks,
Guido


> library(QuasR)
> library(BSgenome)
> library(Rsamtools)
> library(rtracklayer)
> library(GenomicFeatures)
> library(BSgenome.Rnorvegicus.UCSC.rn5)
> sampleFile <- "samples_GH2.txt"
> genomeFile <- "BSgenome.Rnorvegicus.UCSC.rn5"
>
> proj <- qAlign(sampleFile=sampleFile, genome=genomeFile)
alignment files missing - need to:
    create alignment index for the genome
    create 18 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Error in get(genome) : object 'BSgenome.Rnorvegicus.UCSC.rn5' not found
>

# The info is there, so this does work, but it cannot be effectuated in QuasR
> Rnorvegicus
Rat genome
|
| organism: Rattus norvegicus (Rat)
| provider: UCSC
| provider version: rn5
| release date: Mar. 2012
| release name: RGSC 5.0
|
| single sequences (see '?seqnames'):
|   chr1   chr2   chr3   chr4   chr5   chr6   chr7   chr8   chr9   chr10  chr11
|   chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr20  chrX   chrM
|
| multiple sequences (see '?mseqnames'):
|   random        chrUn         upstream1000  upstream2000  upstream5000
|
| (use the '$' or '[[' operator to access a given sequence)
> seqlengths(Rnorvegicus)
     chr1      chr2      chr3      chr4      chr5      chr6      chr7      chr8
290094216 285068071 183740530 248343840 177180328 156897508 143501887 132457389
     chr9     chr10     chr11     chr12     chr13     chr14     chr15     chr16
121549591 112200500  93518069  54450796 118718031 115151701 114627140  90051983
    chr17     chr18     chr19     chr20      chrX      chrM
 92503511  87229863  72914587  57791882 154597545     16313
>

> genomeFile <- "Rnorvegicus"
> proj <- qAlign(sampleFile=sampleFile, genome=genomeFile)
The specified genome is not a fasta file or an installed BSgenome.
Connecting to Bioconductor and searching for a matching genome (internet connection required)...OK
Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
Error: Rnorvegicus is not available in Bioconductor. Type available.genomes() for a complete list
>

> sessionInfo()
R Under development (unstable) (2013-11-19 r64265)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] BiocInstaller_1.13.3                 BSgenome.Rnorvegicus.UCSC.rn5_1.3.17
[3] GenomicFeatures_1.15.7               AnnotationDbi_1.25.9
 [5] Biobase_2.23.5                       rtracklayer_1.23.14
 [7] Rsamtools_1.15.29                    BSgenome_1.31.12
 [9] Biostrings_2.31.14                   XVector_0.3.7
[11] QuasR_1.3.12                         Rbowtie_1.3.0
[13] GenomicRanges_1.15.31                IRanges_1.21.32
[15] BiocGenerics_0.9.3

loaded via a namespace (and not attached):
[1] BatchJobs_1.2             BBmisc_1.5
 [3] BiocParallel_0.5.8        biomaRt_2.19.3
 [5] bitops_1.0-6              brew_1.0-6
 [7] codetools_0.2-8           DBI_0.2-7
 [9] digest_0.6.4              fail_1.2
[11] foreach_1.4.1             GenomicAlignments_0.99.26
[13] grid_3.1.0                hwriter_1.3
[15] iterators_1.0.6           lattice_0.20-24
[17] latticeExtra_0.6-26       plyr_1.8.1
[19] RColorBrewer_1.0-5        Rcpp_0.11.0
[21] RCurl_1.95-4.1            RSQLite_0.11.4
[23] sendmailR_1.1-2           ShortRead_1.21.14
[25] stats4_3.1.0              stringr_0.6.2
[27] tools_3.1.0               XML_3.98-1.1
[29] zlibbioc_1.9.0
>


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