[ensembl-dev] Streaming BAM files in IGV

[Fields, Christopher J]

Regarding GTF in igv, igv works much faster if the GTF/GFF is sorted and indexed (particularly large GTF/GFF).  At least this is what I typically do when annotating large genomes.   Maybe that would help?  I believe it takes either tabix index or igvtools-based (which may or may not be tabix-compatible, so beware).

(BTW this also follows for BED, though I suggest converting to BigBed for that)

chris

On Mar 7, 2014, at 3:11 AM, Andy Yates <ayates at ebi.ac.uk<mailto:ayates at ebi.ac.uk>> wrote:

Hi Genomeo

So firstly looking at the information at igv it can only render tracks hosted on http. Those files are on FTP only. Without locally downloading it you won't be able to visualise. We are looking into making this available on http but I cannot give any firm timelines.

Secondly I did manage to load the gtf in igv (did it about 2 weeks ago) but it took 4gb and ages to load. Like cup of coffee timescales but it did work in the end. The solution here would be to use an alternative format such as bigBed. We don't make the genes available in that format at the moment but I am working towards making this happen. We recognise how important this is with so many new browsers now available we need yo make it easier to access Ensembl data and in particular the gene sets.

As an alternative you could always download bed from the rest api's region endpoint (http://beta.rest.ensembl.org/documentation/info/feature_region) so long as you can work in smaller regions (5mb). Or you could attach the Ensembl das source which igv says it can understand. There's info from http://www.ensembl.org/info/data/ensembl_das.html

Hope this helps a little

Andy

Sent from my tablet

On 6 Mar 2014, at 18:13, Genomeo Dev <genomeodev at gmail.com<mailto:genomeodev at gmail.com>> wrote:

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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