One slight correction. If you are talking about using bigWig
and bigBed files locally in a mirror installation, yes, they
can be used as files locally and do not need to be URL resources.
The 'loading' of the file into the database is merely a one
column entry into its tableName database table, for example:
hgsql hg19 -e 'drop table if exists myLocalBigWig; \
create table myLocalBigWig (fileName varchar(255) not null); \
insert into myLocalBigWig values
("/gbdb/hg19/bbi/myLocalBigWig.bw");'
The entry in the trackDb.ra file is just like a 'type wig min max'
except it is now 'type bigWig min max'
Note comments in the hg/makeDb/trackDb/README file about this.
--Hiram
Hiram Clawson wrote:
> bigWig (and bigBed) files must be URL resources. They are not files to be
> passed whole to our server. The benefit is the saving in transport
> time. Only the bits that are needed for a particular view in
> the browser are transported as needed. The bits transferred accumulate
> in a cache at our end so that subsequence views of the same data
> require no transfer at all.
>
> --Hiram
>
> David Hoover wrote:
>> While we're talking about this, is it possible to upload a bigWig file
>> into custom tracks using the same mechanism as a wig file, or must the
>> file be on a remote server and accessed through a URL?
>>
>> Hiram Clawson wrote:
>>> Good Morning David:
>>>
>>> Are you talking about the database contents of
>>> the wiggle data, or the source ascii files that
>>> are given to wigEncode ?
>>>
>>> If they are just the source ascii files, they
>>> can all go together with 'cat':
>>> $ cat files*.wig > result.wig
>>>
>>> If they have custom track and browser lines in them:
>>> $ egrep -v "^track|^browser" files*.wig > result.wig
>>>
>>> Or, all these can be sent into wigEncode:
>>> $ egrep -v "^track|^browser" files*.wig | wigEncode stdin result.wig
>>> result.wib
>>>
>>> We now try to distinguish source files with the suffix:
>>> .wigFixed or .wigVar
>>> for fixedStep or variableStep wiggle ascii data.
>>>
>>> You may also be interested in the more efficient
>>> encoding mechanism of wigToBigWig and the resulting .bw
>>> file which can be a URL resource. See also:
>>> http://genome.ucsc.edu/goldenPath/help/bigWig.html
>>> This encoder works for bedGraph file types too and is
>>> much more efficient:
>>> http://genome.ucsc.edu/goldenPath/help/bedgraph.html
>>>
>>> --Hiram
>>>
>>> David Hoover wrote:
>>>> I have multiple .wig files, one for each chromosome. Is there source
>>>> code for an executable to concatenate the .wig files into a single
>>>> .wig file?
>>>>
>>>> David Hoover
>>>> Helix Systems Staff
>>>> http://helix.nih.gov
>
> _______________________________________________
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
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