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
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
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
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
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 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
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
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
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
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