Hi Ricardo, 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. Best, J. On Feb 8, 2013, at 2:28 PM, Perez, Ricardo wrote: > Hello, > > I am getting this error when using Extract Genomic DNA (version 2.2.2) > > empty > 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 > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/
___________________________________________________________ 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: http://lists.bx.psu.edu/
