[BioC] Retreving mRNA subsequence (GenomicFeatures, BSgenome)
guest at bioconductor.org
Tue Oct 15 18:36:42 CEST 2013
Problem summary: How to retrieve part of the sequence of mRNA around given location.
I have the locations of the binding to mRNA events as GRanges (GRevents) and need to retrieve sequence for motif finding. The problem is that if I use getSeq(flank(GRevents, width=n)) then I get the genomic sequence not transcript sequence, i.e. not accounting for introns or mRNA border. I have tried solving it with exonsBy("transcriptDb object", "tx") function but without success.
Question: Is there a bioconductor-supported way of getting resolving the problem? With CLIPseq being more and more popular this will be very demanded function.
-- output of sessionInfo():
R version 2.15.0 (2012-03-30)
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=C LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 rtracklayer_1.16.0 GenomicFeatures_1.8.1
 AnnotationDbi_1.18.4 Biobase_2.16.0
 BSgenome.Mmusculus.UCSC.mm9_1.3.17 BSgenome_1.24.0
 Biostrings_2.24.1 GenomicRanges_1.8.3
 IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
 biomaRt_2.12.0 bitops_1.0-4.1 DBI_0.2-5 RCurl_1.91-1
 Rsamtools_1.8.0 RSQLite_0.11.1 stats4_2.15.0 tools_2.15.0
 XML_3.9-4 zlibbioc_1.2.0
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