[ensembl-dev] Streaming BAM files in IGV

Genomeo Dev genomeodev at gmail.com
Mon Mar 10 10:02:14 GMT 2014


Thanks Andy.

1) Just to confirm. Are you able to load this file into IGV from URL?

ftp://ftp.ensembl.org/pub/release-75/data_files/homo_sapiens/GRCh37/rnaseq/GRCh37.HumanBodyMap.brain.1.bam

If yes, do you paste this link as ftp:// or http:// in the URL box?

2) When you mentioned 'I've tried sorting on a local GTF file but to little
success without it taking up a lot of RAM', you actually were not able to
sort the file as opposed to having sorted it and not been able to load it
into IGV. Am I right? How much memory are you using with IGV?

Thanks,



On 8 March 2014 11:48, Andy Yates <ayates at ebi.ac.uk> wrote:

> Hi,
>
> Apologies from my initial reading of their docs it seemed that there was
> no support for FTP. I have been able to load our BAMs into a local IGV
> instance so I don't think there is a problem here. It was probably related
> to our FTP issues yesterday.
>
> As for loading the models I've tried sorting on a local GTF file but to
> little success without it taking up a lot of RAM. So at the moment I would
> suggest using the DAS track for the gene annotations & using the flat files
> for the RNA-seq data. If we can manage to make something better we will let
> you know.
>
> Andy
>
> On 7 Mar 2014, at 11:20, Genomeo Dev <genomeodev at gmail.com> wrote:
>
> > 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:
> >
> >       * Select File>Load from URL.
> >       * 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.
> >> _______________________________________________
> >> Dev mailing list    Dev at ensembl.org
> >> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> >> Ensembl Blog: http://www.ensembl.info/
> >
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
> >
> >
> >
> > --
> > G.
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>



-- 
G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140310/894c116a/attachment.html>


More information about the Dev mailing list