May I ask for your opinion on the importance of having the read number correctly embedded in the FastQ headers?
Are there tools that rely on those patterns or you do take a look when receiving new FastQs from the sequencing facility?
I am asking, because we started to use kits that have a UMI embedded in the sequencing adapter, which is read before the second read and output into a separate FastQ file. Because we output the UMI before the second read,
bcl-convert will embed the read number
2 into the UMI reads and
3 into the headers of the mate reads.
Therefore, we ponder how big of an issue this will be, e.g. cause malfunction with downstream tools and confuse bioinformaticians? Should the read number in your opinion be changed back to e.g.
/2 or would
/3 be fine as well?
Sharing your opinion on this would be greatly appreciated! Thanks a lot