Stephen,

This is a formatting issue with your input file; it needs to be tab-delimited but it's not currently. You'll need to:

(a) convert spaces to tabs using the "Convert delimiters to Tabs" tool; (b) click on the pencil icon and set the data type to BED.

Best, J.

On Jun 21, 2011, at 8:45 AM, Stephen Taylor wrote:

Hi,

I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server:

chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821

I got the following galaxy output:

====================================

7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240"

Any ideas what I am doing wrong?

Thanks,

Steve ___________________________________________________________ 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:

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Hi Stephen,

In your original dataset, there are extra spaces around the tabs. Where "^I" indicates a tab and "$" indicates an end-of-line character, the entire datafile looks like this:

chr5 ^I 47258168 ^I 47259240$ chr18 ^I 1938527 ^I 1939965$ chr2 ^I 101973625 ^I 101974007$ chr4 ^I 75653898 ^I 75674045$ chr19 ^I 4258837 ^I 4263299$ chr4 ^I 39330049 ^I 39372715$ chr4 ^I 9606881 ^I 9610083$ chr15 ^I 7264937 ^I 7265599$ chr21 ^I 6659189 ^I 6667015$ chr2 ^I 351239 ^I 352821$

This could have been introduced in many ways, which is why the tools in Text Manipulation can be so handy. Hopefully this helps!

Best,

Jen Galaxy team

On 6/21/11 7:58 AM, Stephen Taylor wrote:

Hi Jeremy,

...

This is a formatting issue with your input file; it needs to be tab-delimited but it's not currently. You'll need to:

(a) convert spaces to tabs using the "Convert delimiters to Tabs" tool; (b) click on the pencil icon and set the data type to BED.

Thanks, this works, but as a user I cannot see (but obviously you can :-)) that there is a difference between my original and the one I did step (a) and (b) on. I thought I had uploaded a bed file and converted tabs to spaces.

The data is shared here:

http://main.g2.bx.psu.edu/u/stephentaylor/h/test

"Not working" is my original

"Working" is the new data that I did (a) and (b) on.

What did I miss?

Thanks,

Steve

...

Best, J.

On Jun 21, 2011, at 8:45 AM, Stephen Taylor wrote:

...

Hi,

I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server:

chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821

I got the following galaxy output:

====================================

7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240"

Any ideas what I am doing wrong?

Thanks,

Steve ___________________________________________________________ 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/

---

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/

Hi John,

Currently, these come from the UCSC Genome Browser's download area. http://hgdownload.cse.ucsc.edu/downloads.html

AXT files usually come from the primary data source. UCSC provides tools to create NIB, 2bit, etc. files from fasta (found under "Source" section, same link as above). If you have other genomes not in their primarily vertebrate dataset that you want to use with tools that require these formats, the tools would allow you to create your own.

The Galaxy team, too, has been discussing creating files like this for a wider range of genomes, but no specific plans are in place yet.

Please let us know if we can help more,

Best,

Jen Galaxy team

On 6/21/11 10:24 AM, John David Osborne wrote:

Hi Jen,

Where do you get your AXT or NIB files in order to do the extract genome operation? I understand that extract genomic DNA is dependent on those files and correct paths/files in AlignSec.loc?

This is for our local instance of Galaxy.

-John

---

From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Jennifer Jackson [jen@bx.psu.edu] Sent: Tuesday, June 21, 2011 10:23 AM To: Stephen Taylor Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Extract Genomic DNA Problem

Hi Stephen,

In your original dataset, there are extra spaces around the tabs. Where "^I" indicates a tab and "$" indicates an end-of-line character, the entire datafile looks like this:

chr5 ^I 47258168 ^I 47259240$ chr18 ^I 1938527 ^I 1939965$ chr2 ^I 101973625 ^I 101974007$ chr4 ^I 75653898 ^I 75674045$ chr19 ^I 4258837 ^I 4263299$ chr4 ^I 39330049 ^I 39372715$ chr4 ^I 9606881 ^I 9610083$ chr15 ^I 7264937 ^I 7265599$ chr21 ^I 6659189 ^I 6667015$ chr2 ^I 351239 ^I 352821$

This could have been introduced in many ways, which is why the tools in Text Manipulation can be so handy. Hopefully this helps!

Best,

Jen Galaxy team

On 6/21/11 7:58 AM, Stephen Taylor wrote:

...

Hi Jeremy,

...

This is a formatting issue with your input file; it needs to be tab-delimited but it's not currently. You'll need to:

(a) convert spaces to tabs using the "Convert delimiters to Tabs" tool; (b) click on the pencil icon and set the data type to BED.

Thanks, this works, but as a user I cannot see (but obviously you can :-)) that there is a difference between my original and the one I did step (a) and (b) on. I thought I had uploaded a bed file and converted tabs to spaces.

The data is shared here:

http://main.g2.bx.psu.edu/u/stephentaylor/h/test

"Not working" is my original

"Working" is the new data that I did (a) and (b) on.

What did I miss?

Thanks,

Steve

...

Best, J.

On Jun 21, 2011, at 8:45 AM, Stephen Taylor wrote:

...

Hi,

I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server:

chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821

I got the following galaxy output:

====================================

7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240"

Any ideas what I am doing wrong?

Thanks,

Steve ___________________________________________________________ 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/

---

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/

-- Jennifer Jackson http://usegalaxy.org/ 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/

Hi all,

i am not sure if this is the right forum.

but i need as much access to start up information on the system for developers.

we are part of a group in Kenya trying to come up with some apps on a gnome sequencing project we are starting here.

regards

Hi Fabian,

Please see the Galaxy wiki for help getting started: http://bitbucket.org/galaxy/galaxy-central/wiki/Home

Just in case you don't have the link, this is the public Galaxy web site: http://usegalaxy.org

Best!

Jen Galaxy team

On 6/22/11 3:56 AM, Fabian Owuor wrote:

Hi all,

i am not sure if this is the right forum.

but i need as much access to start up information on the system for developers.

we are part of a group in Kenya trying to come up with some apps on a gnome sequencing project we are starting here.

regards