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Question: problems with "fetch data"
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gravatar for as2272
3.1 years ago by
as2272 • 0
United Kingdom
as2272 • 0 wrote:

HI, I am trying to extract some genomic sequences using the Fetch data tool but I keep getting this error:

Using *.nib genomic reference files 15 warnings, 1st is: Unable to fetch the sequence from '85570188' to '300' for chrom ' chr6'. Skipped 15 invalid lines, 1st is #1, " chr6 85570188 85570488 NM_145223 0 -"

 

can you please advise?

 

best

 

Alessandra

 
software error • 779 views
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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by as2272 • 0
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is an older genome? The target genome at UCSC might not have the appropriate files the Data Manager is expecting. 

What you can do:

  1. If there is a fasta.gz file available, use that for the genome. It can be loaded directly into a history under your admin account.
  2. Download the 2bit (if available) or nib files (if that is the only choice) locally to your computer. Then using UCSC's tools (see their "Download" page under Source http://genome.ucsc.edu), create a fasta file for the data and load directly into a history under your admin account.
  3. As the final step, add the genome using the Data manager with the option to use as input a fasta file from a history.

Hopefully this helps! Jen, Galaxy team

 
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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