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