Possible Bug In Fastx Toolkit

Question

[Abhi]

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@?=??. ########################################################################
#########

Answer 1

[Pierre Lindenbaum]

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.

[Zev.Kronenberg]

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

[Abhi]

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