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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