Hey guys,
I have a similar issue with loading BAM track. I have indexed and
sorted files, as described in help page for bam
(http://genome.cse.ucsc.edu/goldenPath/help/bam.html). My track info in
trackDb_user.ra file looks as follows
-------------------------------------------------------------
track bamexample
type bam
shortLabel BAM example
longLabel BAM example
priority 8
visibility pack
db Phatr2
baseColorUseSequence lfExtra
baseColorDefault diffBases
showDiffBasesAllScales .
showDiffBasesMaxZoom 100
indelDoubleInsert on
indelQueryInsert on
bigDataUrl http://subdomain.domain.edu/bam/filename_sorted.bam
------------------------------------------------------------
Next I ran hgTrackDb
>hgTrackDb ORGNAME DBNAME trackDb_user ../../lib/trackDb.sql .
this produces trackDb_user.tab file which has some track info as
described above but not all, i:e the url indicated for bigDataUrl does not
exist in trackDb_user.tab file. When I view the browser I get following error,
No load handler for bam data; possible missing trackDb `type'
or `subTrack' attribute.
Any thoughts? am I missing something?
Jaysheel
On Jun 21, 2010, at 5:30 PM, Mary Goldman wrote:
> Hi Dave,
>
> The track and browser lines are not in the BAM/SAM file - they are
> entered into the "Paste URLs or data" text box on the custom track page
> here: http://genome.cse.ucsc.edu/cgi-bin/hgCustom. The browser line is
> not required; however, as it says in the BAM help page
> (http://genome.cse.ucsc.edu/goldenPath/help/bam.html), you *must* have a
> track line that, at a minimum, defines the track type and the bigDataUrl
> (example of full track line: track type=bam
> bigDataUrl=http://myorg.edu/mylab/my.sorted.bam).
>
> You would only need to download samtools if you need to modify the BAM
> file, which is not needed if you are simply trying to display the data
> in the Genome Browser.
>
> I hope this information is helpful. Please feel free to contact the
> mail list again if you require further assistance.
>
> Best,
> Mary
> ------------------
> Mary Goldman
> UCSC Bioinformatics Group
>
> On 6/21/10 5:16 AM, David A. wrote:
>> Hi there!
>> sorry for a basic question, but I am finding different kind of information
>> regarding this matter. I would like to load two BAM files aligned to the
>> mouse genome from two different samples, so around 500Mb per sample. I have
>> checked the BAM track format and am trying to follow the examples but I am
>> getting lost.
>> The guide says that I have to modify the BAM file in order to add browser
>> lines and track lines. I think that the browser lines are not necessary, but
>> how about the track lines? How can I modify the BAM file? Do I have to
>> convert it to SAM, modify it and then convert it back to BAM?
>>
>> Also, searching on the mailing list, I have found that I have to install
>> samtools C library. Is this necessary?
>>
>> Can I just specify the URL where these two files are stored (together with
>> the corresponding bam.bai files) and just press load?
>>
>> Thanks for your help,
>>
>> Dave
>>
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