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

[sanjay s. <bea...@gm...>]

Hi Mitch,

Thanks .But do that error really hampers the functionality of BAM files
being visualized in Jbrowse(I mean is there any data ,information loss  due
to this  in BAM to JSON conversion and visualization in Jbrowse.



Thanks,
Sanjay

On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <mit...@be...>wrote:

> Hi,
>
> I've seen this but I haven't yet figured out exactly what's going on.  I
> think it has something to do with paired-end reads, and it might be caused
> by reads whose pair-mate isn't mapped.
>
> Handling paired-end reads better is something I'm currently working on.
>
> Mitch
>
>
> On 06/23/2010 01:35 AM, sanjay shah wrote:
>
>> Hi ,
>>
>>
>> Sorry Typo error in the earlier mail ..
>>
>>    The bam file is "20100311.sorted.bam"  and not "20100311.bam"
>> that is being provided in the command after index has been created  as
>> :
>>   " 20100311.sorted.bam.bai ."..
>> So the command  executed is :
>>  $$ bin/flatfile-to-json.pl  --bam
>>   /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass
>> exon
>>   --tracklabel BAM_data --key "BAM Data"
>>
>>
>>  which   throws the  following error
>>
>> Use of uninitialized value in int at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>>
>>
>> please help ..Thanks
>>
>> Thanks,
>> Sanjay
>>
>>
>>
>>
>> Thanks,
>> Sanjay
>>
>> On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<bea...@gm...>  wrote:
>>
>>
>>> Hi ,
>>>
>>> Thanks.I  did sort  the alignments and  then  created index manually
>>> with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
>>> again try to convert BAM to JSON by issuing command as:
>>>
>>>
>>>  $$ 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  following error:
>>>
>>> Use of uninitialized value in int at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>>> Use of uninitialized value in subtraction (-) at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>>> Use of uninitialized value in int at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>>> Use of uninitialized value in subtraction (-) at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>>> Use of uninitialized value in int at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>>> Use of uninitialized value in subtraction (-) at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>>> Use of uninitialized value in int at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>>> Use of uninitialized value in subtraction (-) at
>>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>>>
>>>
>>>
>>> Please help on this aspect ..Thanks
>>>
>>>
>>> Thanks,
>>> Sanjay
>>>
>>>
>>> On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
>>> <mit...@be...>  wrote:
>>>
>>>
>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Success is how many times u smile each day every day.
>>>
>>>
>>>
>>
>>
>>
>>
>
>


-- 
Success is how many times u smile each day every day.