This tool requires external data that you'll need to configure. Here's how:
(1) download the 2bit file from UCSC for your genomes into a local directory
from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
(2) add an entry like this to alignseq.loc (note that you'll need to use tabs
to separate the columns:
seq hg19 /galaxy/data/hg19/seq/hg19.2bit
(3) try running the tool again.
On Feb 8, 2013, at 2:28 PM, Perez, Ricardo wrote:
> I am getting this error when using Extract Genomic DNA (version 2.2.2)
> format: fasta, database: hg19
> 924 warnings, 1st is: Chromosome by name 'chr22' was not found for build
> 'hg19'. Skipped 924 invalid lines, 1st is #1, "chr22 16256331 16287937
> NM_001136213 0 - 16258185 16287885 0 11
> 346,119,167,45,71,71,138,107,174,115,684, 0,1853,10597,11805,13541,188
> We set up a local instance of Galaxy and a local mirror of the UCSC Table
> browser in our servers.
> Thank you for your help,
> --Ricardo Perez
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: