Hi Kory,

The problem with this FASTQ block is that the sequence and quality score 
identifier lines do not match ('SNPSTER6_0679:1:1:1083:939#0/1 
run=100908_SNPSTER6_0679_70929AAXX' vs 'SNPSTER6_0679:1:1:1083:939#0/1'), where 
the identifier for the sequence line has additional text not found on the 
identifier for the quality score line, which is not valid for the FASTQ format. 
Alternatively the quality score identifier line could be only a '+', without 
the sequence identifier.

The quality score lines appear to be either illumina or solexa, but it is best 
to check with the source of the data to be sure:
Input ASCII range: 'B'(66) - '_'(95)
Input decimal range: 2 - 31

You'll need to upload valid FASTQ files inorder to work with them in Galaxy. 
Correct examples of your provided read are:

@SNPSTER6_0679:1:1:1083:939#0/1
NATTTATGGATAGTTGGGTAGTAGGTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAA
+SNPSTER6_0679:1:1:1083:939#0/1
BIQQIQQQTP[[[[[VVVVQPPPPPTWWWW[[YYTTTOVV____TWVXRWPTQPQWWWWWTOOVV___V_TROOWTWTWTQWQWTTRWRO

or

@SNPSTER6_0679:1:1:1083:939#0/1 run=100908_SNPSTER6_0679_70929AAXX
NATTTATGGATAGTTGGGTAGTAGGTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAA
+
BIQQIQQQTP[[[[[VVVVQPPPPPTWWWW[[YYTTTOVV____TWVXRWPTQPQWWWWWTOOVV___V_TROOWTWTWTQWQWTTRWRO

or

@SNPSTER6_0679:1:1:1083:939#0/1 run=100908_SNPSTER6_0679_70929AAXX
NATTTATGGATAGTTGGGTAGTAGGTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAA
+SNPSTER6_0679:1:1:1083:939#0/1 run=100908_SNPSTER6_0679_70929AAXX
BIQQIQQQTP[[[[[VVVVQPPPPPTWWWW[[YYTTTOVV____TWVXRWPTQPQWWWWWTOOVV___V_TROOWTWTWTQWQWTTRWRO

Please let us know if we can be of further assistance.

Thanks for using Galaxy,

Dan


On Feb 2, 2011, at 2:01 PM, Johnson, Kory (NIH/NINDS) [C] wrote:

> Hello,
>  
> My account login is: johnso...@ninds.nih.gov
>  
> I am a first time Galaxy user.
>  
> I have uploaded my sequences as format “fastq” into Galaxy and would like to 
> next use “Groomer” to output Sanger fastq format so to go on with exploring 
> quality via box plot, deciding on a trim length (if any), and map to genome 
> using bwa or bowtie.
>  
> However, I am running into a problem using “Groomer”.
>  
> I do not know what format my sequences are per setting the required input 
> parameter.
>  
> An example of my sequences is as follows:
>  
> @SNPSTER6_0679:1:1:1083:939#0/1 run=100908_SNPSTER6_0679_70929AAXX
> NATTTATGGATAGTTGGGTAGTAGGTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAA
> +SNPSTER6_0679:1:1:1083:939#0/1
> BIQQIQQQTP[[[[[VVVVQPPPPPTWWWW[[YYTTTOVV____TWVXRWPTQPQWWWWWTOOVV___V_TROOWTWTWTQWQWTTRWRO
>  
> … how to tell if you have: “Sanger”, “Solexa”, “Illumina 1.3+”, etc.
>  
> I have tried to submit to “Groomer” different times using these options one 
> at a time and none return with results.
>  
> Need help please.
>  
> Also, what is the expected time for “Groomer” to return results for a file 
> containing 2.7 million reads.
>  
> Thank you … best,
>  
> Kory
>  
> --------------------------------------------
>  
> Kory R. Johnson, MS, PhD
> Sr. Bioinformatics Scientist
>  
> <image001.jpg>
>  
> www.kellygovernmentsolutions.com
>  
> Providing Contract Services For:
>  
> Bioinformatics Section,
> Information Technology & Bioinformatics Program,
> Division of Intramural Research (DIR),
> National Institute of Neurological Disorders & Stroke (NINDS),
> National Institutes of Health (NIH),
> Bethesda, Maryland
>  
> Mailing Address:
>  
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>  
> Contact Information:
>  
> Phone:    301-402-1956
> Fax:           301-480-3563
> email:       johnso...@ninds.nih.gov
>  
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