How to deal the paired-end data

[zhaocheng3326]

From the 4C-ker paper, we know "For paired-end sequencing experiments the read containing the bait and the primary restriction enzyme was mapped as single-end data" . Is it meaning we should treat the paired-end data as single-end data ?

[R-PatricioMonteiro]

Hey!

I have this question too.
My data was sequenced with paired-end and I want to use this package but I not know how to deal with paired-end sequencing with R.4C-ker package.

Can you help me?

Thanks, R

[rr1859]

Hi,

If this is not allele specific 4C then you can just use the read that contains the primer sequence and treat is as single-end sequencing.

[R-PatricioMonteiro]

So, your suggestion is not consider the fastq file R2 and only use the R1 that contain the primer sequence?

Thanks for the quick answer!