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Old 09-10-2012, 08:07 AM   #1
WaltL
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Default FastX-Toolkit qual_filter error

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
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Old 09-10-2012, 08:30 AM   #2
JQL
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You need to specify -Q33.
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Old 09-10-2012, 08:35 AM   #3
WaltL
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Quote:
Originally Posted by JQL View Post
You need to specify -Q33.
Ahhhhh, thank you... that worked!
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Old 09-10-2012, 10:09 AM   #4
JQL
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are you going to use fastx_clipper? Let me know how that works for you.

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Originally Posted by WaltL View Post
Ahhhhh, thank you... that worked!
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Old 09-10-2012, 11:05 AM   #5
WaltL
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Quote:
Originally Posted by JQL View Post
are you going to use fastx_clipper? Let me know how that works for you.
I'm trying some different tools out to see which works best. I've used FastQC to identify problems and adapter seqs in the reads. Next, I used cutadapter to trim, and now I'm trying the fastq qual trimmer. I will probably try the fastx_clipper, but some of my colleagues use Cutadapt and they really like it for speed, and it seems to have a bit better documentation that the FastX suite. I'll post once I see how things work out for this dataset.
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