Question: .wig files for strand-specific paired-end RNA-Seq
6.5 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi, Is there a simple way to make strand-specific .wig file (i.e., a separate track for + and - strand) from paired-end data (where the second read maps to the other strand)? I've tried using this: library(Rsamtools) library(rtracklayer) myReads <- readGappedAlignments("RNAseqMapping.bam") coveragePlus <- coverage(myReads[strand(myReads) == '+']) export(coveragePlus, "RNAplus.wig") coverageMinus <- coverage(myReads[strand(myReads) == '-']) export(coverageMinus, "RNAminus.wig") But it appears that the second read in the pair contributes to the other strand, generating similar tracks for the + and the - strands. Is there a way to deal with this better? Thanks! Igor. -- output of sessionInfo(): R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  tools_2.13.1 -- Sent via the guest posting facility at bioconductor.org.
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