[ensembl-dev] Streaming BAM files in IGV

[Genomeo Dev]

Hi,

There are other things in Ensembl which I want to use inside igv, not just
the annotations such as RNAseq and Epigenetic data, hence I have been
looking at loading from URL. Well, based on this IGV documentation, IGV
also accepts ftp:

Load from URL

To load data from an HTTP URL:

   1. Select *File>Load* from URL.
   2. Enter the HTTP or FTP URL for a data file or sample information file,
   then click *OK*.

http://www.broadinstitute.org/igv/loaddata

For the other question, would it be safe for me to do the gtf to bigBed
conversion myself?

G.

On 7 March 2014 09:11, Andy Yates <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> 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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-- 
G.
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