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  • .wig files for strand-specific paired-end RNA-Seq

    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)? genomeCoverageBed doesn't seem to handle this well. Any alternatives?

    Igor.

  • #2
    It's quick using R with the packages Rsamtools, GenomicRanges, and rtracklayer.

    Code:
    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")

    Comment


    • #3
      Thanks! But this appears to suffer from the same problem as genomeCoverageBed - I get similar coverage on both strands, because if the transcript is on the + strand, read #2 maps to the - strand, and contributes to the coverage on the - strand... Is there any way around this?

      Comment


      • #4
        Good point. You should ask about it on the Bioconductor mailing list. They implement feature requests quickly.

        Comment


        • #5
          Just flip the strand of the #2 reads

          Comment

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