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
<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqtofasta%2Ffastq_to_fasta_python%2F1.0.0>
converter, the fastq file can be detected.
On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning
<[email protected] <mailto:[email protected]>> 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,
> <[email protected]
<mailto:[email protected]>> wrote:
> Send galaxy-user mailing list submissions to
> [email protected] <mailto:[email protected]>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.bx.psu.edu/listinfo/galaxy-user
> or, via email, send a message with subject or body 'help' to
> [email protected]
<mailto:[email protected]>
>
> You can reach the person managing the list at
> [email protected]
<mailto:[email protected]>
>
> When replying, please edit your Subject line so it is more
> specific
> than "Re: Contents of galaxy-user digest..."
>
>
> HEY! This is important! If you reply to a thread in a
> digest, please
> 1. Change the subject of your response from "Galaxy-user
> Digest Vol ..." to the original subject for the thread.
> 2. Strip out everything else in the digest that is not
part of
> the thread you are responding to.
>
> Why?
> 1. This will keep the subject meaningful. People will have
> some idea from the subject line if they should read it
or not.
> 2. Not doing this greatly increases the number of emails
that
> match search queries, but that aren't actually informative.
>
> Today's Topics:
>
> 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 <[email protected]
<mailto:[email protected]>>
> To: graham etherington (TSL)
> <[email protected]
<mailto:[email protected]>>
> Cc: [email protected]
<mailto:[email protected]>
> Subject: Re: [galaxy-user] Creating a Trackster
visualisation
> from a
> reference in your history
> Message-ID:
> <[email protected]
<mailto:[email protected]>>
> 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.
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
>
<http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20140123/4a84218a/attachment-0001.html>
>
> ------------------------------
>
> _______________________________________________
> galaxy-user mailing list
> [email protected] <mailto:[email protected]>
> http://lists.bx.psu.edu/listinfo/galaxy-user
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
> End of galaxy-user Digest, Vol 91, Issue 21
> *******************************************
>
>
>
> --
> 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
> Galaxy analysis and other features on the public server
> at usegalaxy.org <http://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/
>
> To search Galaxy mailing lists use the unified search at:
>
> http://galaxyproject.org/search/mailinglists/
--
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
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
