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 thi
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
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 for
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" , Ex
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.adelphitra
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 75
011 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 "$" indicates an end-of-line character,
the entire
From: galaxy-user-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson
[j...@bx.psu.edu]
Sent: Tuesday, June 21, 2011 10:23 AM
To: Stephen Taylor
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Extract Genomic DNA Problem
Hi Stephen,
In your original
Hi Stephen,
In your original dataset, there are extra spaces around the tabs.
Where "^I" indicates a tab and "$" 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
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 us
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
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
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
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
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
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