Hello Jaysheel,
If you are adding the data as a native track, then no track/browser
lines are needed. Instead, load the data into a table and edit the
trackDb.ra file (as you show). bigDataUrl is not a supported field for
the trackDb.ra file.
For an example of a native BAM track in the browser, see the hg18
trackDb.ra file. This example is a composite track, so ignore that part
of the block formatting. What you want to notice is the "track bam*"
table names in the subtracks. If you bring up these tables in the Table
browser (or in mySQL) you will notice that they are pointers to files in
/gbdb. Model your data like this and the native track should load
without issue.
from kent/src/hg/makeDb/trackDb/human/hg18/trackDb.ra
track oneKGHighCovSeq
compositeTrack on
shortLabel 1kG High-Cov Seq
longLabel 1000 Genomes High-Coverage Individuals Sequence Reads
group x
priority 4.1
visibility hide
type bam
pairEndsByName .
stripPrefix chr
baseColorUseSequence lfExtra
baseColorDefault diffBases
showDiffBasesAllScales .
showDiffBasesMaxZoom 100
chromosomes
chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY
maxWindowToDraw 200000
track bamNA12878 <- model table like this and put data in /gbdb
subTrack oneKGHighCovSeq on
shortLabel NA12878 Slx BAM
longLabel 1000Genomes NA12878 Solexa aligned reads
track bamNA12891
subTrack oneKGHighCovSeq on
shortLabel NA12891 Slx BAM
longLabel 1000Genomes NA12891 Solexa aligned reads
I hope this information is helpful. Please feel free to contact the
help mailing list again if you require further assistance.
Best regards,
Jen
UCSC Genome Browser Support
http://genome.ucsc.edu/contacts.html
[email protected] [email protected]
On 6/21/10 8:41 PM, Jaysheel Bhavsar wrote:
> 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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>
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