JaneliaSciComp/msg — Issue #26: Remove poor quality reads from fastq file right away using TQSfastq.py
Author: gregpinero
Created: 2012-02-14 12:46:50+00:00
State: open

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)