How Can I Filter Out Reads According To Phred Score In Fastq Files?

Question

[sanchezcavani]

I want to filter out reads with general phred score lower than a cutoff. Is there any software that can be used?

Answer 1

[rob234king]

Trimmomatic is very good for trimming and filtering. Fastx toolkit can also be used. If your mapping reads usually better just to set this in the program rather than yourself as improves mapping. For instance novoalign H parameter can be used to clip 3' end of reads by a quality of your choosing while pretrimming gives me worse results.