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:
> 
> 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/

Reply via email to