[Genome] wigmaf-type in trackdb.ra

[Hiram Clawson]

Good Morning Max:

Please take a look at the example conservation track entries
in the source tree trackDb files for assemblies that have
conservation tracks.  For example: src/hg/makeDb/trackDb/human/hg18/trackDb.ra
the 28-way multiz track entry.

That will get your trackDb entry correct.

For the alignments to display, your maf files need to be in a /gbdb/
location.  Please note the sequence of loading instructions in
the source tree make docs, for example, the 28-way loading
in src/hg/makeDb/doc/hg18.txt:

>    # load tables for a look
>     ssh hgwdev
>     mkdir -p /gbdb/hg18/multiz28way/maf
>     ln -s /cluster/data/hg18/bed/multiz28way/maf/*.maf \
>                 /gbdb/hg18/multiz28way/maf
>     cd /cluster/data/hg18/bed/multiz28way
>     hgLoadMaf -pathPrefix=/gbdb/hg18/multiz28way/maf hg18 multiz28way
>      # load summary table
>      cat maf/*.maf |  nice hgLoadMafSummary hg18 -minSize=30000 -mergeGap=1500 \
>                  -maxSize=200000  multiz28waySummary stdin


Note how the /gbdb/ symlinks are made to the actual maf files.
And then the pathPrefix command in the hgLoadMaf business
to properly point to them.

--Hiram

Maximilian Haeussler wrote:
> Dear gurus,
> 
> I've aligned C. intestinalis and C. savingyi some time ago and wrote a
> how-to about it (
> http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto).
> Tried to do blastz/chain/netting/maffing and loaded the mafs into the
> browser. The alignments look nice when I zoom to basepair resolution.
> 
> However, the wigmaf-track doesn't seem to be recognized as a maf-track: When
> I click onto it, no alignments are displayed and the table browser doesn't
> offer the "maf" format for download.
> I have no clue where to search, can you give me a hint into the right
> direction?
> 
> Example:
> http://genome.ciona.cnrs-gif.fr/cgi-bin/hgTracks?hgt.out1=1.5x&position=chr10p%3A958170-959006
> 
> Thanks a lot in advance,
> Max