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
___________________________________________________________
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
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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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
