Adding New Tracks to a browser installation

Adding a custom track

See Also

For a generic discussion of how to load any type of track into your local browser mirror, refer to the document in the source tree src/product/README.trackDb and the discussion of how the trackDb entries function in src/hg/makeDb/trackDb/README

Gotchas

Your .bed file better not have any browser or track lines if you want the loader to work

You need to hop all over the source tree like a frog on a griddle to get things done...

The docs are a little misleading perhaps. I seemed to need a .hg.conf file in my home directory - setting env options didn't seem to help a bit for commandline building access.

A BED track description for a custom SNP track

The .bed file has lines like this:

chr22   49512530        49512531        rs8137951       0       +       49512530        49512531        255,0,0
chr22   49518559        49518560        rs756638        0       +       49518559        49518560        255,0,0
chr22   49522492        49522493        rs3810648       0       +       49522492        49522493        255,0,0
chr22   49524956        49524957        rs2285395       0       +       49524956        49524957        255,0,0
chrX    100017093       100017094       rs5921682       0       +       100017093       100017094       255,0,0
chrX    100019802       100019803       rs5967204       0       -       100019802       100019803       255,0,0

Load the .bed file into a custom track called Ill550v3 Note the .bed file must have NO browser or track lines - otherwise hgLoadBed will barf

/var/www/cgi-bin/loader/hgLoadBed -noBin  -tab hg18 Ill550v3 /home/rerla/public_html/illHH550v3.BED

Adjust your trackDb.ra file

I'm working (eg) on meme in

/home/rerla/hg18/kent/src/hg/makeDb/trackDb/human/hg18

I add these settings - they seem to work the way I want, allowing the name field from the .bed file to appear in full view:

track Ill550v3
priority 20.1   
shortLabel Illum550kv3           
longLabel Illumina 550k v3 snps
visibility pack
type bed 9 .          
color 255,0,0   
group varRep                 
thickDrawItem on

Recompile the trackDb

make alpha DBS=hg18