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epgg / eg

EpiGenome Gateway - WashU EpiGenome Browser
http://epigenomegateway.wustl.edu/legacy/
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local install not loading sequence track #61

Open rakarnik opened 7 years ago

rakarnik commented 7 years ago

Our local install of the browser shows "Cannot open sequence file", unlike the WashU browser that shows the DNA sequence. How do we fix this?

Also, is it possible to download the sequence in text or FASTA format?

lidaof commented 7 years ago

Hi @rakarnik do you have the sequence fasta file bgzip'ed and tabix'ed?

if not, you need use this script https://github.com/epgg/script/blob/master/fa2tabix.py and put generated files under /srv/epgg/data/data/subtleKnife/seq/

let me know if this helps. thanks.

rakarnik commented 7 years ago

Hi Daofeng, Do the output files need to be named a certain way under /srv/epgg/data/data/subtleKnife/seq/? Say for hg19? Thanks! Any ideas about how users can download sequence for a region in the browser?

lidaof commented 7 years ago

Hi @rakarnik, yes, the name should be match the genome assembly, say hg19.gz and hg19.gz.tbi. this was controlled by makeDb.sql file: bbiPath and seqPath. check this https://github.com/epgg/eg/blob/master/config/hg19/makeDb.sql please.

for the get sequence function, we don't have this feature yet, will try to implement it in near future release.

Thanks.

rakarnik commented 7 years ago

Thanks Daofeng, I will try that and report back to confirm that it solved the issue.