Question: Possible Bug In Fastx Toolkit
3
gravatar for Abhi
6.7 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

I am getting the following error with fastx_quality_stats with version 0.0.13.2. May be this has to do with the changing Illumina scores. Now they are Phred33 I believe. Has anyone seen this issue

fastx_quality_stats -i test.fastq 
fastx_quality_stats: Invalid quality score value (char ')' ord 41 quality value -23) on line 4

Thanks! -Abhi

more test.fastq 
@HISEQ08:235:D142MACXX:7:1101:1474:2097 1:N:0:CGATGT
CCCTCTCCTTCTCCCAGGTAGAACGAGCCTCCCTTTCCCTAGTCAGGGAGTCTTCAAGGAGTTTCTCCTTTGCTGCTGACTTGTCTTTGAATTGCTTGTGGCGTTTTGGAACTTCCTCTTCATTAAGAATCTAGGGTTGTG
CAATTTTCT
+
??<DDD=:C>:CC@A@EEE@C:4:F)@?EDDDD3?B??B9?B?9BD3@@@BC>@CEIIEA=C@?=??. ########################################################################
#########
fastq fastx • 6.7k views
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 6.7 years ago by Abhi1.5k
11
gravatar for Pierre Lindenbaum
6.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

A quick google returns: http://seqanswers.com/forums/archive/index.php/t-7596.html

ou need to add the -Q33 parameter to tell it that you're using Illumina encoded quality scores, not Sanger encoding.

ADD COMMENTlink written 6.7 years ago by Pierre Lindenbaum124k
11

They do need better documentation on the -Q33 flag. It took me too long to hunt down that flag.

ADD REPLYlink written 6.7 years ago by Zev.Kronenberg11k
1

I agree ..-Q33 is nowhere mentioned in the docs...thanks guys

ADD REPLYlink written 6.7 years ago by Abhi1.5k
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