Hi, I just notice that NGS FASTQ Trimmer<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_trimmer%2Ffastq_trimmer%2F1.0.0>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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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 <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/117fef56513fc563dd231516...
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.
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: Send galaxy-user mailing list submissions to galaxy-user@lists.bx.psu.edu
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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 <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/117fef56513fc563dd231516...
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.
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 <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: 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-request@lists.bx.psu.edu
You can reach the person managing the list at galaxy-user-owner@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 <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/117fef56513fc563dd231516...
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.
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_T... 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 <bjoern.gruening@gmail.com <mailto: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 <mailto:galaxy-user-request@lists.bx.psu.edu>> wrote: > Send galaxy-user mailing list submissions to > galaxy-user@lists.bx.psu.edu <mailto: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-request@lists.bx.psu.edu <mailto:galaxy-user-request@lists.bx.psu.edu> > > You can reach the person managing the list at > galaxy-user-owner@lists.bx.psu.edu <mailto:galaxy-user-owner@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 <jgoecks@email.gwu.edu <mailto:jgoecks@email.gwu.edu>> > To: graham etherington (TSL) > <graham.etherington@sainsbury-laboratory.ac.uk <mailto:graham.etherington@sainsbury-laboratory.ac.uk>> > Cc: galaxy-user@lists.bx.psu.edu <mailto: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 <mailto: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/117fef56513fc563dd231516... > > 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. > >
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 <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: 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-request@lists.bx.psu.edu
You can reach the person managing the list at galaxy-user-owner@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 <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/117fef56513fc563dd231516...
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.
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 <bjoern.gruening@gmail.com <mailto: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 <mailto:galaxy-user-request@lists.bx.psu.edu>> wrote: > Send galaxy-user mailing list submissions to > galaxy-user@lists.bx.psu.edu <mailto: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-request@lists.bx.psu.edu <mailto:galaxy-user-request@lists.bx.psu.edu> > > You can reach the person managing the list at > galaxy-user-owner@lists.bx.psu.edu <mailto:galaxy-user-owner@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 <jgoecks@email.gwu.edu <mailto:jgoecks@email.gwu.edu>> > To: graham etherington (TSL) > <graham.etherington@sainsbury-laboratory.ac.uk <mailto:graham.etherington@sainsbury-laboratory.ac.uk>> > Cc: galaxy-user@lists.bx.psu.edu <mailto: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 <mailto: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/117fef56513fc563dd231516... > > 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. > >
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 <jen@bx.psu.edu> 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 <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: 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-request@lists.bx.psu.edu
You can reach the person managing the list at galaxy-user-owner@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 <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/117fef56513fc563dd231516...
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.
participants (3)
-
Björn Grüning -
Gang Wang -
Jennifer Jackson