Hello, Bill,
You must make an index (samename.bai) from your BAM file
using Samtools and place it in the same directory. The URL
should then work as you have it.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 12/1/2011 12:19 PM, Sean Davis wrote:
> Hi, Bill.
>
> I'm not a UCSC person, but I did take a quick look at your data using:
>
> samtools idxstats http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam
>
> It appears from this output that the VAST majority of your reads are not
> mapped. That probably explains why you do not see any data since, on
> average, it appears that only a few hundred reads are on any chromosome.
>
> Hope that helps.
> Sean
>
>
> On Thu, Dec 1, 2011 at 3:04 PM, William Noble <[email protected]>wrote:
>
>> Hi,
>>
>> We are trying to view a BAM file at UCSC, created by Bowtie followed by
>> Samtools. The file is visible on the web at
>>
>> http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam
>>
>> However, when we upload this to the mm9 genome in the custom track page,
>> using this track line
>>
>> track type=bam db=mm9
>> bigDataUrl=http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam
>>
>> we don't actually see any data in the browser. When we instead upload
>> the file directly, using the "Browse..."/"Upload" option, we get an
>> error message that says "*Error Can't read file: s_6_1.bam*".
>>
>> Since BAM is not text-based, it's not easy to figure out how to debug
>> this. Can anyone help us figure out what's wrong with our file?
>>
>> Bill
>>
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>
> _______________________________________________
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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