Mapping of paired end chipseq reads with Bowtie2 gives error

Question

[yansh111]

Hi All

I am trying to map paired end data with Bowtie 2, it shows

Error, fewer reads in file specified with -2 than in file specified with -1

Please help me to solve this problem.

Yogesh

Answer 1

[Devon Ryan]

There error message in this case says exactly what the problem is. I'm guessing that you used something like fastx tools, that can't handle paired-end reads, to quality and adapter trim your reads. If you use trimmomatic, trim_galore, or something similar then this won't happen.

Anyway, the simplest way to resync the files is to use repair.sh that comes with BBMap. You can see Brian Bushnell give an example of that here.