Question: problems with "fetch data"
0
gravatar for as2272
3.1 years ago by
as22720
United Kingdom
as22720 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
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by as22720
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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