Can FourCSeq packages handle the alignment with paired-end library?
If it is, is it OK to follow the normal workflow (such as in vignettes example)?
FourCSeq was not designed to work with paired end reads. You could try to map each side separately however this might result in fragments which get counted twice.
Could you clarify whether the reads all should start and end in restriction enzyme cutting sites in your protocol?
Thanks a lot. I also guess that it is not desigend to do, but to make sure, I asked.
Yes, one read of pair starts with primer + first or second restriction enzyme site and another read starts with diff primer + second or first restriction enzyme site.
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