Re: [Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

[Mitch S. <mit...@be...>]

In the future, JBrowse will probably use the autoindexing option as 
suggested by that error message.

Right now, though, you can get around this by creating the index 
manually with samtools; you'd write something like:

$ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam

(using the full path to the samtools program if it's not in your path)

Mitch

On 06/22/2010 02:12 AM, sanjay shah wrote:
> Hi,
>
> I have a BAM file   and when i execute the following command  to
> convert the BAM to Json :
>
> $$ bin/flatfile-to-json.pl  --bam
> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
> --tracklabel BAM_data --key "BAM Data"
>
> I get the following error;
>
> No index file for
> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
> 1940
>
> I have installed the  prerequisite installed for browsing BAM files in
> Jbrowse .I also have  the corresponding reference file in Json  and am
> able to browse in Jbrowse.
>
>
> Do we have to create any index for browsing BAM files in Jbrowse
> before we convert it to Json .Please help  me in resolving the
> following error.
>
>
>
> Thanks,
> Sanjay
>
>