fastq files from pair-end sequencing, for 4c-seq analysis, How to analyze ?

Question

[htchd7ji]

Hi,

I have fastq files from pair-end sequencing, for 4c-seq/Chip-seq analysis. How to analyze it?

The data contains R1 and R2 fastq files. Should I merge them? All the pipelines I found on the web use single-end sequencing, how to modify my data to fit those type of analysis?

Thanks

[ATpoint]

You can simply use only R1 which would be the same as single-end sequencing. From there on, follow the published pipelines. In any case, you should not merge them as the R2 is simply the other end of the fragment sequenced by R1, so merging would artificially double the number of reads without adding information. It is certainly possible to analyze 4C-seq with paired-end information but if you are unexperienced I suggest you limit to R1 and follow the protocols.

[htchd7ji]

Thank you. I'll try R1