Howdy, Rich,
My interpretation of the error report is that the fastq file you are
trying to groom contains the indicated text (lab/solexa_public/Zon/
111021_WICMT-SOLEXA_64KF7AAXX/QualityScore/s_3_1_sequence.txt) on a
line where it expects a valid fastq header. I believe a valid header
line would begin with an at sign ("@"). So perhaps somewhere along
the way, your fastq file's contents were replaced by a filename.
Bob H
On Nov 2, 2011, at 10:09 AM, Richard Mark White wrote:
Hi,
So, I am getting a fastq groomer error on some illumina data, with
the following error. any ideas?
There was an error reading your input file. Your input file is
likely malformed.
It is suggested that you double-check your original input file for
errors -- helpful information for this purpose has been provided
below.
However, if you think that you have encountered an actual error with
this tool, please do tell us by using the bug reporting mechanism.
The reported error is: 'Invalid fastq header: lab/solexa_public/Zon/
111021_WICMT-SOLEXA_64KF7AAXX/QualityScore/s_3_1_sequence.txt
rich
From: Jennifer Jackson <j...@bx.psu.edu>
To: arabidopsis <svine...@gmail.com>
Cc: galaxy-user@lists.bx.psu.edu
Sent: Wednesday, November 2, 2011 9:19 AM
Subject: Re: [galaxy-user] fastq groomer
Hello Slon,
In case you are still having issues, the best use case for Illumina
1.8+
data is to run the FASTQ Groomer tool with the option "Sanger". As
Peter
noted, this assigns the expected datatype plus verifies content before
investing time in downstream analysis.
Please let us know if more help is needed,
Best,
Jen
Galaxy team
On 10/18/11 1:02 AM, arabidopsis wrote:
> Hi all,
>
> Fastq groomer has Solexa or Illumina 1.3+ as an input quality
format. I
> asked at the sequencing facility about their machine and output
and they
> said their format was Illumina 1.8+ (the newest). I tried to
convert my
> fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an
input
> option and got all reads with quality of around 10... Does it mean
that
> Galaxy cannot be used on a dataset with 1.8+ encoding or something
else
> was wrong?
>
> Thanks,
>
> Slon
>
>
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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