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Old 02-03-2012, 01:21 PM   #1
weasteam
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Default How to filter FASTQ Quality?

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.
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Old 02-04-2012, 02:09 AM   #2
cahillcahill
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Detect & remove sequencing adapters and primers
Detect limited skewing at the ends of reads and clip
Detect poor quality at the ends of reads and clip
Detect N's, and remove from ends
Remove reads with CASAVA 'Y' flag (purity filtering)
Discard sequences that are too short after all of the above
Keep multiple mate-reads in sync while doing all of the abov
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Old 04-24-2012, 08:14 AM   #3
fznajar
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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
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Old 04-24-2012, 10:12 AM   #4
westerman
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Quote:
Originally Posted by fznajar View Post
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.
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Old 04-24-2012, 10:19 AM   #5
ETHANol
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Quote:
Originally Posted by fznajar View Post
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.
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