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Question: alignseq.loc and the use of 2bit files
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gravatar for Ian
3.8 years ago by
Ian • 10
United Kingdom
Ian • 10 wrote:

The alignseq.loc file only mentions the use of .nib files.  Can anyone confirm whether .2bit files can be used instead?

Thank you.
nib alignseq 2bit • 1.1k views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by Ian • 10
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, .2bit files can be used. Here are some example lines:

seq    mm7    /galaxy/data/mm7/seq/mm7.2bit
seq    mm8    /galaxy/data/mm8/seq/mm8.2bit
seq    mm9    /galaxy/data/mm9/seq/mm9.2bit
seq    mm10   /galaxy/data/mm10/seq/mm10.2bit

For more examples you can take a look at the alignseq.loc we use on the public Main Galaxy instance. It can be obtained from the rsync server's "location" directory. Instructions here:
http://wiki.galaxyproject.org/Admin/UseGalaxyRsync

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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