Fail to map after clip adaptor

Question

[mht.tsai]

Dear all,

I recently got several exomes but the FastQC suggested that there might be adaptor sequencing contamination showed on Kmer content. I used clip adaptor and filter the read by quality but then I when I try to use BWA to align, it failed.

If I use non-clip fastq, BWA works. Any suggestion how to fix this problem?

Or perhaps, it doesn't matter as the contaminated reads will not be aligned properly anyway?

Thanks for your opinion or suggestion in advance.

HankT

[Dan D]

How does BWA fail? Can you post the error message?

Also, what are you using for trimming and filtering? Posting the command lines you used for all of operations would also help us.

My best guess right now is that the the trimming/filtering process is ruining the read pairing between the two files. The nth read in the FASTQ file for read 1 should be the mate of the nth read in the FASTQ file for read 2.

[mht.tsai]

Thanks Dan for answering my question,

Sorry I deleted the history so I cannot post the error message. but I think you are probably right. The error message showed something seems to be mismatch of reads. If that is the case, how can I avoid this situation. when pre-processing? I used trimming by sliding window and filter by quality on Galaxy.

Hank T

[Dan D]

I see. I haven't used Galaxy in ages. I bet you'll get a quality, quick answer by asking at the Galaxy Biostar.

Outside of Galaxy, I would use PE-aware trimming programs, like sickle (for quality trimming) or cutadapt (for adapter and/or quality trimming).