Re: [galaxy-user] Extract genomic DNA

[Jeremy Goecks]

Rebecca,

You should be able to use a custom genome with this tool by selecting "History" 
from the "Source for Genomic Data" parameter.

The bug you're describing has, to the best of my knowledge, been fixed in 
Galaxy and should not be present anymore. On which Galaxy instance are you 
seeing this issue? If this is not the main Galaxy server ( 
http://main.g2.bx.psu.edu/ ), you'll want to contact the maintainers of the 
instance that you're using and ask them to update the instance.

Best,
J.

On Dec 14, 2011, at 1:31 PM, Rebecca C Mueller wrote:

> Hi all,
> Does anyone know if you can use the "Extract Genomic DNA" command with a 
> genome not in the database? I am working with an algal genome (C. merolae) 
> that isn't currently in the pulldown Database/Build menu. I keep getting the 
> "Unspecified genome build" error, and am assuming that's the problem, as my 
> other files appear to be formatted correctly (tab delimited without spaces 
> for the intervals, same names for chromosomes in interval and fasta file, 
> etc).
> Thanks!
> Rebecca
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[galaxy-user] Extract genomic DNA

[Rebecca C Mueller]

Hi all,
Does anyone know if you can use the "Extract Genomic DNA" command with 
a genome not in the database? I am working with an algal genome (C. 
merolae) that isn't currently in the pulldown Database/Build menu. I 
keep getting the "Unspecified genome build" error, and am assuming 
that's the problem, as my other files appear to be formatted correctly 
(tab delimited without spaces for the intervals, same names for 
chromosomes in interval and fasta file, etc).

Thanks!
Rebecca
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Re: [galaxy-user] Extract genomic DNA-strand information is not recognized

[Jennifer Jackson]

Hi Sarah,

One of the specifications of BED format is that the coordinates are with 
respect to the forward strand.


BED format originated at UCSC, and this is their full specification:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

And Galaxy's summary (also on tool forms that accept BED format):
http://galaxyproject.org/wiki/Learn/Datatypes#Bed

The rules to transform data in other coordinate formats to BED is 
explained in detail in this UCSC wiki document: 
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms


There are no Galaxy wrapped automated tools to do this transformation, 
but perhaps someone on the mailing list has a workflow to offer. If not, 
the tools in Galaxy under "Text Manipulation" and "Filter and Sort" and 
a file containing the length of each chromosome can very likely be used 
in combination to perform the calculations (in several steps). If you 
create a process to do this, be sure to considering publishing the 
workflow for others to use.


Hopefully this helps,

Best,

Jen
Galaxy team

On 10/24/11 7:20 PM, Sarah wrote:

Hello,

I am trying to extract sequences from a FASTA file containing genomic
information. The coordinates are in a tab-delimited format, which is
recognized as BED format by Galaxy (meaning that the 6th column is
correctly interpreted as 6. Strand).

However, upon running "Fetch sequences" , Extract Genomic DNA only the
+-strand information is included in the output FASTA file and I receive
the following ERROR message:

1,431 sequences
format: fasta, database: ?

Info: 1476 warnings, 1st is: Invalid interval, start '1616' > end '1177'.
Skipped 1476 invalid lines, 1st is #2, "scaffold1 1616 1177 Fom - 1"

Is this a bug? How can I can adjust my input data files to get the
--strand sequences as well?

I have seen a similar problem in an earlier posting and there it was
suggested to manually adjust the strand information column 5, but this
did not work for me neither.

Many thanks for your all help!


Sarah


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[galaxy-user] Extract genomic DNA-strand information is not recognized

[Sarah]

Hello,

I am trying to extract sequences from a FASTA file containing genomic 
information. The coordinates are in a tab-delimited format, which is recognized 
as BED format by Galaxy (meaning that the 6th column is correctly interpreted 
as 6. Strand).

However, upon running "Fetch sequences" , Extract Genomic DNA only the +-strand 
information is included in the output FASTA file and I receive the following 
ERROR message:

1,431 sequences
format: fasta, database: ?
Info: 1476 warnings, 1st is: Invalid interval, start '1616' > end '1177'. 
Skipped 1476 invalid lines, 1st is #2, "scaffold1   16161177Fom -   
1"

Is this a bug? How can I can adjust my input data files to get the --strand 
sequences as well?

I have seen a similar problem in an earlier posting and there it was suggested 
to manually adjust the strand information column 5, but this did not work for 
me neither.

Many thanks for your all help!


Sarah___
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Re: [galaxy-user] Extract Genomic DNA Problem

[Fabian Owuor]

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
-- 
Fabian .J. Owuor
> 
> www.adelphitrading.co.ke | www.iHub.co.ke (red member)
> www.four99.co.ke | www.fabian.me.ke | www.epiphany.co.ke
> Yu: +254 753.333.824 | Safaricom: +254 721.948.852 | Skype: kootie
> Orange: +254 772.189.962 | Airtel: +254 735.270.852 | tweet: @theusfab

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Re: [galaxy-user] Extract Genomic DNA Problem

[Stephen Taylor]

Hi jen,


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!



Ah I see. Thanks for the tip.

Steve


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
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Re: [galaxy-user] Extract Genomic DNA Problem

[Jennifer Jackson]

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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson 
[j...@bx.psu.edu]
Sent: Tuesday, June 21, 2011 10:23 AM
To: Stephen Taylor
Cc: galaxy-u...@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
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http://usegalaxy.org/
http://galaxyproject.org/
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Re: [galaxy-user] Extract Genomic DNA Problem

[John David Osborne]

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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson 
[j...@bx.psu.edu]
Sent: Tuesday, June 21, 2011 10:23 AM
To: Stephen Taylor
Cc: galaxy-u...@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/
>>
>
> ___
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> use the Galaxy Development list:
>
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>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/

--
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http://usegalaxy.org/
http://galaxyproject.org/
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Re: [galaxy-user] Extract Genomic DNA Problem

[Jennifer Jackson]

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
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http://usegalaxy.org/
http://galaxyproject.org/
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Re: [galaxy-user] Extract Genomic DNA Problem

[Stephen Taylor]

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 4725816847259240
chr181938527 1939965
chr2 101973625   101974007
chr4 7565389875674045
chr194258837 4263299
chr4 3933004939372715
chr4 9606881 9610083
chr157264937 7265599
chr216659189 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
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Re: [galaxy-user] Extract Genomic DNA Problem

[Jeremy Goecks]

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   4725816847259240
> chr18  1938527 1939965
> chr2   101973625   101974007
> chr4   7565389875674045
> chr19  4258837 4263299
> chr4   3933004939372715
> 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
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> http://lists.bx.psu.edu/


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[galaxy-user] Extract Genomic DNA Problem

[Stephen Taylor]

Hi,

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

chr5 4725816847259240
chr181938527 1939965
chr2 101973625   101974007
chr4 7565389875674045
chr194258837 4263299
chr4 3933004939372715
chr4 9606881 9610083
chr157264937 7265599
chr216659189 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
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[galaxy-user] Extract Genomic DNA Problem

[Steve Taylor]

Hi,

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

chr5 4725816847259240
chr181938527 1939965
chr2 101973625   101974007
chr4 7565389875674045
chr194258837 4263299
chr4 3933004939372715
chr4 9606881 9610083
chr157264937 7265599
chr216659189 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
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Re: [galaxy-user] extract genomic DNA

[Jeremy Goecks]

Hello,

We recently updated our main server and a bug was introduced to this tool.
This bug has been fixed in our main repository, and we'll update our server
in the next day or so to fix this bug.

Thanks,
J.

On Mon, Feb 14, 2011 at 5:24 PM, Keith E. Giles  wrote:

> a few days ago I was able to extract genomic DNA from a bed file in
> either fasta or interval format. But today, that same file, and
> subsets of that larger file are giving me errors.  It doens't tell me
> much.  What is so incredibly frustrating is that the datasets are
> identical!!!  One day they seem to work, the  next not.  Any ideas?
> ___
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> and
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> list:
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[galaxy-user] extract genomic DNA

[Keith E. Giles]

a few days ago I was able to extract genomic DNA from a bed file in
either fasta or interval format. But today, that same file, and
subsets of that larger file are giving me errors.  It doens't tell me
much.  What is so incredibly frustrating is that the datasets are
identical!!!  One day they seem to work, the  next not.  Any ideas?
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