Remove poor quality reads from fastq file right away using TQSfastq.py

[gregpinero]

Run the reads file through TQSfastq.py. Make this optionial and configurable.

Peter or David:

TQSfastq.py has these options, what do you think the default values should be?

Phred quality threshold: Base intensity threshold value (Phred quality scores 0 to 40, default=10)

consec: Minimum number of consecutive bases passing threshold values (default=20)

ASCII encoding type: Type of ASCII encoding: 33 (standard) or 64 (illumina) (default=64)

[gregpinero]

Peter recommends these defaults:

I recommend that we go with QV>=20 and demand 30 consecutive bases. I have seen systematic problems using the 20 consecutive bp default.

[gregpinero]

Question, do we want to filter only the reads.fq file or also the parent reads? I'm assuming all.

[gregpinero]

Note to self:

msg/TQSfastq.py -f reads.fq -t 20 -c 30 -q -z -o reads.fq creates: reads.fq.trim.fastq