Closed mrvollger closed 2 years ago
Hi Mitchell,
are you suggesting that the bases of unpolished sequences (sequences outputted when using -u
) are all lowercase or would you like to have lowercase bases in both polished and unpolished sequences?
Sorry for the late response! Best regards, Robert
Hi Robert,
I was suggesting that when -u
is used that unpolished bases are lowercase, and polished bases are uppercase, or perhaps a new flag with this behavior. If it helps convince you this is the defualt now used by the PacBio polishers https://github.com/PacificBiosciences/GenomicConsensus/blob/develop/doc/FAQ.rst#what-does-it-mean-that-quiver-consensus-is-de-novo. It is not a big deal, but it is helpful in downstream analysis to be able to make separate quality scores for polished and unpolished bases, and lower/upper case makes that distinction easy.
No worries.
Best, Mitchell
Just a suggesting an enhancement.
When using
-u
it would be nice if unpolished bases were lowercase.Best, Mitchell