Thank again Dave, For anyone who is interested, I've written a script for converting the 2bit's into fa's here: https://bitbucket.org/gvl/gen_loc_files
Also packaged is a script to generate loc files by traversing the rsynced folder, there is more work to be done on it though. All feedback/contributions are welcome! Kevin On Wed, Sep 26, 2012 at 11:26 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > Kevin, > > We decided to exclude fasta files mainly because 2bit is a lossless > compression with a much lower file size, so it would be a waste of our > users' bandwidth and time to include the (approximately) four times larger > files when 2bit is available. > > --Dave B. > > > On 9/25/12 20:55:31.000, Kevin Y wrote: > >> Thanks Dave, >> A question before we go ahead, why are they missing in the first place? >> >> Does the main galaxy not actually need them? are the tools moving away >> from fa? >> >> Cheers, >> Kevin. >> >> On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier <d...@bx.psu.edu >> <mailto:d...@bx.psu.edu>> wrote: >> >> Kevin, >> >> Correct, converting from 2bit to fasta shouldn't cause any problems. >> >> --Dave B. >> >> >> On 9/25/12 03:20:14.000, Kevin Y wrote: >> >> Hi, >> >> Thanks for providing the indexes via rsync:: >> >> http://wiki.g2.bx.psu.edu/__**Admin/Data%20Integration<http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration> >> >> >> <http://wiki.g2.bx.psu.edu/**Admin/Data%20Integration<http://wiki.g2.bx.psu.edu/Admin/Data%20Integration> >> > >> >> We've, noticed that despite soft links pointing to it, there are >> no .fa >> files for example in hg19/seq/ >> However there are 2bit files. >> >> Would you guys recommend we convert them from 2bit to fasta? >> >> Thanks, >> Kevin. >> >> >> ______________________________**______________________________**_ >> >> 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/ >> >> >>
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