Question: Data Files
gravatar for Alastair Kerr
9.7 years ago by
Alastair Kerr30 wrote:
Hi, first a quick word of thanks to the galaxy devs: this is a great system thanks, we are using it to roll-out our own in-house tools/scripts. We are now in the about to gather the UCSC data files so that the rest of the tools (liftover, Fetch sequences/alignments etc) work. I am wondering whether there is an easy way of gathering this data? e.g. are there any wget /rsync scripts available or does each data source need to be added manually. thanks - Alastair -- Alastair Kerr, Ph.D., Bioinformatician, Wellcome Trust Centre for Cell Biology, 2.21, Michael Swann Building, Kings buildings, The University of Edinburgh, Edinburgh, EH9 3JR, UK Tel: 44-(0)131-650-7527 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
galaxy • 661 views
ADD COMMENTlink modified 9.7 years ago by Nate Coraor3.2k • written 9.7 years ago by Alastair Kerr30
gravatar for Nate Coraor
9.7 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:
Hi Alastair, We don't really have an easy way to do this, as the data comes from a wide number of sources, made available via different methods. That said, I did write a perl script a few years ago to download sequences and alignments from UCSC. Note that it only downloads the axt's, and Galaxy now uses maf for pairwise alignments. --nate
ADD COMMENTlink written 9.7 years ago by Nate Coraor3.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour