I would like to trim my Illumina RNA-Seq PE data based on one of the following:
- mean/median PHRED score (either for the whole read or over a moving window) or
- Richard Mott's algorithm
I also would like that the program removes a read pair if after trimming one (or both) reads are cut below certain (user-defined) threshold length.
I know there are tons of trimming scripts doing some of the above. Can you point me to a script that meets both requirements (trimming and read pair removal)?