Re: [galaxy-user] NGS Fastq Trimmer error

[Gang Wang]

Hi Jennifer,
I reload my data with defined format type fastqsanger and it works now.
Thank you so much for your help.

Gang


On Thu, Feb 13, 2014 at 6:06 PM, Jennifer Jackson  wrote:

>  Hi Gang,
>
> I can't comment about a PC (I use a MAC), but this shouldn't matter. If
> you are using a local Galaxy (http://getgalaxy.org
> http://usegalaxy.org/toolshed), most tools will follow the same usage
> rules as when implemented on the public Main Galaxy instance at
> http://usegalaxy.org, the Galaxy CloudMan ami, and the bulk of other
> public Galaxy instances, at least for common tools.
>
> Exceptions would be if the tool(s) were specifically modified to function
> differently. Galaxy is open source and variations exist. The tool form of
> any alternate version (of a tool named the same) will likely note what
> modifications have been made. Plus you can always contact the other public
> instance hosts, if you have usage problems.
>
> Best!
>
> Jen
> Galaxy team
>
>
> On 2/13/14 2:26 PM, Gang Wang wrote:
>
>  By the way, can you use detect the fastq file using trimmer by column
> with your PC. Thanks a lot.
>
>
>  Gang
>
>
> On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning 
> 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,
>> >  wrote:
>> > Send galaxy-user mailing list submissions to
>> > galaxy-user@lists.bx.psu.edu
>> >
>> > 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
>> > galaxy-user-requ...@lists.bx.psu.edu
>> >
>> > You can reach the person managing the list at
>> > galaxy-user-ow...@lists.bx.psu.edu
>> >
>> > 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 
>> > To: graham etherington (TSL)
>> > 
>> > Cc: galaxy-user@lists.bx.psu.edu
>> > Subject: Re: [galaxy-user] Creating a Trackster visualisation
>> > from a
>> > reference in your history
>> > Message-ID:
>> > 
>> > 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
>> > galaxy-user@lists.bx.psu.edu
>> > http://lists.bx.psu.edu/listinfo/galaxy-user
>> >
>> >

Re: [galaxy-user] NGS Fastq Trimmer error

[Jennifer Jackson]

Hi Gang,

I can't comment about a PC (I use a MAC), but this shouldn't matter. If 
you are using a local Galaxy (http://getgalaxy.org 
http://usegalaxy.org/toolshed), most tools will follow the same usage 
rules as when implemented on the public Main Galaxy instance at 
http://usegalaxy.org, the Galaxy CloudMan ami, and the bulk of other 
public Galaxy instances, at least for common tools.


Exceptions would be if the tool(s) were specifically modified to 
function differently. Galaxy is open source and variations exist. The 
tool form of any alternate version (of a tool named the same) will 
likely note what modifications have been made. Plus you can always 
contact the other public instance hosts, if you have usage problems.


Best!

Jen
Galaxy team

On 2/13/14 2:26 PM, Gang Wang wrote:
By the way, can you use detect the fastq file using trimmer by column 
with your PC. Thanks a lot.



Gang


On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning 
mailto:bjoern.gruen...@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,
> mailto:galaxy-user-requ...@lists.bx.psu.edu>> wrote:
> Send galaxy-user mailing list submissions to
> galaxy-user@lists.bx.psu.edu 
>
> 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
> galaxy-user-requ...@lists.bx.psu.edu

>
> You can reach the person managing the list at
> galaxy-user-ow...@lists.bx.psu.edu

>
> 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 mailto:jgoe...@email.gwu.edu>>
> To: graham etherington (TSL)
> mailto:graham.ethering...@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:
> mailto:c3382f38-d243-4979-b6a7-ba13ef161...@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.
>
> -- next part --
> An HTML attachment was scrubbed...
> URL:
>


>
> -

Re: [galaxy-user] NGS Fastq Trimmer error

[Jennifer Jackson]

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 
mailto:bjoern.gruen...@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,
> mailto:galaxy-user-requ...@lists.bx.psu.edu>> wrote:
> Send galaxy-user mailing list submissions to
> galaxy-user@lists.bx.psu.edu 
>
> 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
> galaxy-user-requ...@lists.bx.psu.edu

>
> You can reach the person managing the list at
> galaxy-user-ow...@lists.bx.psu.edu

>
> 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 mailto:jgoe...@email.gwu.edu>>
> To: graham etherington (TSL)
> mailto:graham.ethering...@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:
> mailto:c3382f38-d243-4979-b6a7-ba13ef161...@email.gwu.edu>>
> Content-Type: text/plain; charset="windows-1252"
>
> > Is it possible to crea

Re: [galaxy-user] NGS Fastq Trimmer error

[Gang Wang]

By the way, can you use detect the fastq file using trimmer by column with
your PC. Thanks a lot.


Gang


On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning 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,
> >  wrote:
> > Send galaxy-user mailing list submissions to
> > galaxy-user@lists.bx.psu.edu
> >
> > 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
> > galaxy-user-requ...@lists.bx.psu.edu
> >
> > You can reach the person managing the list at
> > galaxy-user-ow...@lists.bx.psu.edu
> >
> > 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 
> > To: graham etherington (TSL)
> > 
> > Cc: galaxy-user@lists.bx.psu.edu
> > Subject: Re: [galaxy-user] Creating a Trackster visualisation
> > from a
> > reference in your history
> > Message-ID:
> > 
> > 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
> > galaxy-user@lists.bx.psu.edu
> > 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.  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:
> >
>

Re: [galaxy-user] NGS Fastq Trimmer error

[Gang Wang]

The fastq format is correct, when i use FASTQ to
FASTAconverter,
the fastq file can be detected.


On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning 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,
> >  wrote:
> > Send galaxy-user mailing list submissions to
> > galaxy-user@lists.bx.psu.edu
> >
> > 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
> > galaxy-user-requ...@lists.bx.psu.edu
> >
> > You can reach the person managing the list at
> > galaxy-user-ow...@lists.bx.psu.edu
> >
> > 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 
> > To: graham etherington (TSL)
> > 
> > Cc: galaxy-user@lists.bx.psu.edu
> > Subject: Re: [galaxy-user] Creating a Trackster visualisation
> > from a
> > reference in your history
> > Message-ID:
> > 
> > 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
> > galaxy-user@lists.bx.psu.edu
> > 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.  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 t