In Paired-End Data, If One Read Of The Pair Is Unmapped, Is That Pair Autmoatically Improper?

Question

[mrals89]

Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM file?

Thanks!

Answer 1

[Istvan Albert]

No.

The concept of improper pairing should be banished. This word is just a premature optimization from the times when people did not know better.

It is not defined what proper pair actually means and each aligner may pick its own definition.

[Yongjie Zhang]

I have a similar question. What quality detection, and what kind of trims of raw reads by what programs should be performed before joining paired-end raw reads? I think low-quality parts, potential barcode or primer sequences existed in raw reads should be excluded in advance. Is this right?

[Istvan Albert]

Questions need to be asked individually not as a comment to another question. Far many more people will read those and you'll get better and more relevant answers. We want to keep the content well formed, where one thread deals with one piece of knowledge.