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
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
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