How to filter FASTQ Quality?

[weasteam]

FASTX can do FASTQ Quality Filter (http://hannonlab.cshl.edu/fastx_tool...mmandline.html),

[-q N] = Minimum quality score to keep.
[-p N] = Minimum percent of bases that must have [-q] quality.

May do know usually how do you define the minimum quality score and minimum percent of bases?

Thanks.

[fznajar]

It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
Thanks

[westerman]

It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
Thanks

"New"? Since the FastQ format is not embedded in stone then I suppose there could be a popular new format. Haven't heard of one since Illumina switched gears a year or so ago. Anyway, you were asking about other tools. I am partial to trimmomatic myself.

[ETHANol]

It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
Thanks

There is an option to specify the correct quality score.

I've found fastx to be really slow, so I have switched to Trimmomatic.