Hi Wang,

The assigned format is the issue, as Björn replied. The two tools you are referencing to have different criteria for the input fastq data - one is more stringent than the other with regard to content. Both are fastq format, but the one that requires the more specific fastqsanger datatype assignment also has a dependency on the scaling of the quality scores.

There are two histories in your account, and these will work as good examples.

The larger one has a partial RNA-seq workflow - including trimming. Note that the "format" datatype assignment is "fastqsanger" for the input to these jobs. This is the model you want to follow for most analysis in Galaxy.

In the other history are just a few datasets, one with format as "fastq". This is what you need to change so that it becomes "fastqsanger". In your case, the dataset has quality scores are already scaled to be in Sanger Phred with an ASCII offset of 33 - what is labeled in Galaxy as "fastqsanger", so it can be directly assigned to the datatype. Click on the pencil icon for the dataset, then the 'datatype' tab, choose 'fastqsanger', then remember to save. It will now appear as input to the NGS: QC and manipulation tools that were previously blocked.

More about datasets and dataypes is here, including how to assess original quality score scaling and modify it if needed. Direct assignment of datatype is not always appropriate, and there are important tools (like 'FastQC') that are of great utility when deciding how to prep data.
https://wiki.galaxyproject.org/Support#Dataset_special_cases
https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Dataset_Icons_.26_Text

Hopefully this helps to clear up any confusion!

Thanks,

Jen
Galaxy team

On 2/13/14 11:19 AM, Gang Wang wrote:
The fastq format is correct, when i use FASTQ to FASTA converter, the fastq file can be detected.


On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Wang,

please check if your fastq file is associated with the correct fastq
format, fastqsanger probably.

Cheers,
Bjoern

> Hi,
>
> I just notice that NGS FASTQ Trimmer by column can't detect the fastq
> file I loaded. Anyone knows why. thanks a lot.
>
>
>
> On Fri, Jan 24, 2014 at 11:00 AM,
> <galaxy-user-request@lists.bx.psu.edu> wrote:
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>            1. Re: Creating a Trackster visualisation from a
>         reference in
>               your history (Jeremy Goecks)
>
>
>         ----------------------------------------------------------------------
>
>         Message: 1
>         Date: Thu, 23 Jan 2014 15:49:44 -0500
>         From: Jeremy Goecks <jgoecks@email.gwu.edu>
>         To: graham etherington (TSL)
>                 <graham.etherington@sainsbury-laboratory.ac.uk>
>         Cc: galaxy-user@lists.bx.psu.edu
>         Subject: Re: [galaxy-user] Creating a Trackster visualisation
>         from a
>                 reference in your history
>         Message-ID:
>         <C3382F38-D243-4979-B6A7-BA13EF161EE5@email.gwu.edu>
>         Content-Type: text/plain; charset="windows-1252"
>
>         > Is it possible to create a custom build and use it to view a
>         SAM file without adding the .len and .2bit files in to the
>         Galaxy file system as an administrator?
>
>         Yes, it definitely is.
>
>         > If so, what am I doing wrong?
>
>
>         This is a Galaxy bug which has been fixed in this commit:
>
>         https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd231516196cfd601c1635e2
>
>         We have a release coming up, so this fix will be included in
>         the release and will make it to our public server soon. In the
>         meantime, note that you can use the genome fasta file rather
>         than the len file to create a custom build and everything
>         should work.
>
>         Thanks,
>         J.
>
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>
>
> --
> Gang Wang
> Ph.D. student
> Veterinary Integrative Bioscience
> College of Veterinary Medicine & Biomedical Sciences
> Texas A&M University
> College Station, TX  77843-4458
>
>
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--
Gang Wang
Ph.D. student
Veterinary Integrative Bioscience
College of Veterinary Medicine & Biomedical Sciences
Texas A&M University
College Station, TX  77843-4458

 




___________________________________________________________
The Galaxy User list should be used for the discussion of
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