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

[ulitskyi]

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.

[Dario1984]

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

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")

[ulitskyi]

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?

[Dario1984]

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

[frozenlyse]

Just flip the strand of the #2 reads