[ensembl-dev] Streaming BAM files in IGV

Genomeo Dev genomeodev at gmail.com
Thu Mar 6 18:13:37 GMT 2014


Hi,

(1)

I am trying to use IGV browser to load bam files form this location:

ftp://ftp.ensembl.org/pub/release-75/data_files/homo_sapiens/GRCh37/rnaseq/

But I am getting an error message that not possible to establish SOCKS
proxy connection.

I have found that igv mention that 'for .bam, .tdf, and indexed file
formats the server must support byte-range requests.' (
http://www.broadinstitute.org/igv/loaddata)

I was wondering whether there is any thing from the ensembl server side
that is causing this error.

Thanks.

(2)

I want to load annotation into IGV genome browser from
ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz

But the file is too large to handle at once. Any advice from the Ensembl
browser team on how I should be conducting this operation?

Thanks,

-- 
G.
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