Re: [Gmod-ajax] Add bam with corresponding csi index file

[Colin <col...@gm...>]

Can you describe how you are putting the BAM in JBrowse?

Is it through the Open track dialog box or manually editing the config?

I tested adding via the Open track dialog and it seemed to work

Manually editing it in the config requires adding the config
parameter "csiUrlTemplate": "yourfile.bam.csi" with "urlTemplate":
"yourfile.bam"

Also which version of jbrowse is being used?

Thanks,
-Colin

On Wed, Sep 16, 2020 at 10:43 AM Cyril Libourel <
cyr...@lr...> wrote:

> Helo,
>
>
>
> I am working on Barley genome. This species have long chromosomes leading
> to use csi index files for BAM.
>
> I tried to put BAM + .csi file in my jbrowse but I get error telling me
> that there is no index file.
>
> What can I do to “force” jbrowse to use the csi file as index?
>
>
>
> Thank you very much in advance
>
>
>
> Cyril
>
>
>
> Cyril Libourel, Ph.D.
>
> Postdoctoral researcher
>
> Pôle de Biotechnologies Végétales
>
> Laboratoire de Recherche en Sciences Végétales
>
> UMR 5546 CNRS-UPS
>
> 24 Chemin de Borde Rouge
>
> 31326 Castanet Tolosan
>
> FRANCE
>
>
>
>
> https://www.lrsv.ups-tlse.fr/equipes-de-recherche/symbiose-mycorhizienne-et-signalisation-cellulaire/
>
>
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