search

ucsc-mus-strain-cactus / build_browser

Build a UCSC brower from a progressiveCactus alignment
0 stars 0 forks source link

Make BLAT work for assemblies #14

Open ifiddes opened 9 years ago

diekhans commented 9 years ago

This is problematic because we have to setup new blat server and it would not be appropriate to run them on hgwdev.

Ian Fiddes notifications@github.com writes:

— Reply to this email directly or view it on GitHub.*

joelarmstrong commented 9 years ago

Obviously out of scope for this project, but shouldn't it be possible to

joelarmstrong commented 9 years ago

Whoops, hit the wrong button.

I was going to ask, just out of curiosity, shouldn't it be technically possible to keep blat's index on disk for stuff like mice or the rarely-used genomes? I assume that most of the less popular browsers don't have blat servers because it's prohibitive to keep several GB of memory constantly in use for each genome.

diekhans commented 9 years ago

Yes, that is actually something I suggest to Jim at one time. Use mmap to just open the index.

I don't know the index access patterns, so it might very slow.

Maybe worth an experiment, but they still would not be happy running it on hgwdev.

Joel Armstrong notifications@github.com writes:

Whoops, hit the wrong button.

I was going to ask, just out of curiosity, shouldn't it be technically possible to keep blat's index on disk for stuff like mice or the rarely-used genomes? I assume that most of the less popular browsers don't have blat servers because it's prohibitive to keep several GB of memory constantly in use for each genome.

— Reply to this email directly or view it on GitHub.*