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 <dave@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>

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.

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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 <dave@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 <dave@bx.psu.edu <mailto:dave@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:

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