[genome] bedDetail 12 columns format question

[Enrique Medina-Acosta]

Dear UCSC Genome Browser Developer team,

 

I have a problem formatting BED12 column track files into bedDetail 12 column track files.

 

I regularly use, with great success (!), the bedDetail 6 column format, to get hyperlinked description fields ( information of several features of each item), but for some reason, I don´t get through formatting any BED12 column file into a bedDetail.

 

I searched the UCSC archive for hints, but the query I found (here) did not help me much.   

 

Attached are two examples, one of a working bedDetail 6 column track file and one instance of a BED12 column track file, for which I would like to convert into a bedDetail 12 column track file.

 

What am I missing?

 

Thank you,

 

Enrique

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
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Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
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Tel: +55 22 27397085

[Christopher Lee]

Hello Enrique,

Thank you for your question about turning a bed12 into a bedDetail
custom track. BedDetail format uses either the first 3 standard bed
fields or the first 12 standard bed fields, plus two additional
fields, as explained here:
http://genome.ucsc.edu/FAQ/FAQformat#format1.7

These two additional fields are an ID field, and the second field is a
long description, and can contain HTML, as you have noted in your
example tracks. The problem with the bed12 you shared is that it was
missing the ID field after the blockStarts field.

Additionally, you can use ID field to dynamically generate links to
outside websites, like in the example track from the documentation:

track name=HbVar type=bedDetail description="HbVar custom track"
db=hg19 visibility=3
url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$"
chr11 5246919 5246920 Hb_North_York 2619 Hemoglobin variant
chr11 5255660 5255661 HBD c.1 G>A 2659 delta0 thalassemia


Here "2619" will be substituted where the '$$' is in the URL:
http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&id=$$

There are many more URL substitutions available, as described here:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#url

Please let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute

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