I'm trying to us FastX Toolkit for the first time- running the quality filter on an Illumina sr dataset (1.9 encoding) as follows:
fastq_quality_filter -v -q 30 -p 88 -i input_name.fq -o output_name
However, I get the following error (same error when running fastx stats):
Invalid quality score value (char '#' ord 35 quality value -29) on line 4
Here's the file head:
@FLHBFN1:261:C0AHRACXX:2:1101:1381:2173 1:Y:0:TGACCA
CACGNNATCACTATCTCACCTAGGCTGGACTCCAGCTTGGCGCTTCACTC
+
<<<@##2:@@@@@@??@@@???@???@???@???>???<????8?8???;
A post on this issue from last year http://seqanswers.com/forums/showthread.php?p=49667
suggested that, for Illumina data, this was due to either older software versions, I am current (ver. 0.0.13.2.) or to the qual values being out of range. If the acceptable range is still -15 to 93, then I'm not sure what I can do to solve this.
Any suggestions?
Thanks!
Walt
fastq_quality_filter -v -q 30 -p 88 -i input_name.fq -o output_name
However, I get the following error (same error when running fastx stats):
Invalid quality score value (char '#' ord 35 quality value -29) on line 4
Here's the file head:
@FLHBFN1:261:C0AHRACXX:2:1101:1381:2173 1:Y:0:TGACCA
CACGNNATCACTATCTCACCTAGGCTGGACTCCAGCTTGGCGCTTCACTC
+
<<<@##2:@@@@@@??@@@???@???@???@???>???<????8?8???;
A post on this issue from last year http://seqanswers.com/forums/showthread.php?p=49667
suggested that, for Illumina data, this was due to either older software versions, I am current (ver. 0.0.13.2.) or to the qual values being out of range. If the acceptable range is still -15 to 93, then I'm not sure what I can do to solve this.
Any suggestions?
Thanks!
Walt
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