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Old 07-21-2013, 02:19 AM   #1
nightsun
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Location: china

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Default FastX-Toolkit qual_filter error

I obtain my data from Ion Torrent,but when I use FASTX - Toolkit to exceut quality_filter ,some problem appeared,why ?anyone can help me?
fastq_quality_filter -q 20 -i PGM01.fastq -o test.fastq -v -Q 33
fastq_quality_filter: Invalid quality score value (char 'N' ord 78 quality value 45) on line 360
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Old 07-21-2013, 02:59 AM   #2
JackieBadger
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use Trimmomatic
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Old 07-21-2013, 07:32 AM   #3
GenoMax
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If you did have a space between -Q and 33 then try the command without the space like this:

Code:
$ fastq_quality_filter -q 20 -i PGM01.fastq -o test.fastq -v -Q33
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