Paired end SAM to single end

[jennorocks]

I am performing PAR-CLIP which is typically done using single end however we ran paired because it fit in with our in house set up.

I've mapped the reads (as a pair) with bowtie and generated a SAM file that has the pairs alternating.

However, it seems the program I am using to peak call (PARalyzer) doesn't seem to work with the paired file. I get barely any clusters whereas if I just map the forward reads and use those I get 1000s.

Since these are short reads anyway with almost complete overlap the obvious approach is to just work with R1 but is there any way to combine them so I dont lose the mapping info from having R1 and R2

Hope that makes sense

[jennorocks]

Just for an example, a pair of reads might looks like this in my SAM

NTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCAT NGCCTCACAGCACACCTTCACAGGCTTACAGAAC

So between them theres good overlap but they both add 1 to 2 bases so only using 1 of them loses some information