[BioC] QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5

Hervé Pagès hpages at fhcrc.org
Sun Mar 2 02:57:21 CET 2014


Hi Guido,

When using BioC devel, things can move fast so it's important that
you update your packages often (with biocLite()) in order to keep
everything in sync. In your case it looks like the version of the
BSgenome package you have (1.3.17) is lagging behind the version
currently in BioC devel (1.3.99).

Note that starting with BioC 2.14 (which will be released in April,
but corresponds to BioC devel at the moment), many BSgenome packages
exist in 2 flavors: raw genome or masked genome. For example,
for rn5, there is now

   BSgenome.Rnorvegicus.UCSC.rn5              raw genome
   BSgenome.Rnorvegicus.UCSC.rn5.masked       masked genome

BSgenome.Rnorvegicus.UCSC.rn5.masked is equivalent to the old
BSgenome.Rnorvegicus.UCSC.rn5 in BioC <= 2.13 which was already
masked. However, in BioC <= 2.13, there was no non-masked version
of rn5. See announcement here for more details:

   https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005150.html

I don't know if QuasR cares about the masks though. Maybe they're
just ignored, in which case I guess you could just stick to 
BSgenome.Rnorvegicus.UCSC.rn5.

Cheers,
H.


On 02/28/2014 03:44 PM, Hooiveld, Guido wrote:
> 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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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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