Dear list,

Let's say I have single-end strand-specific RNA-Seq data.
Then I could read in the data with:

library(GenomicRanges)

> reads = readGappedAlignments("data.bam")

As I typically don't know which strand has been sequenced, it might be necessary to flip the strand of the reads before doing any kind
of summarizeOverlap:

> strand(reads) = ifelse(strand(reads) == "+", "-", "+")

Now I could do a 'summarizeOverlaps' between the reads and any kind of transcript database. 

Now, if I have paired-end strand-specific RNA-Seq data.
I read the data:
> reads = readGappedAlignmentPairs("data.bam")

How can I flip the strand of the reads? As it's now paired-end data, it does not work as above.
I could imagine several work-arounds, I just wonder if there is any straight approach which I miss at the moment..


best regards,
Stefanie





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