BED Details Format question

[Vikram Katju]

Please find enclosed as a screenshot the first row of my data file which i wish to format in the BED Details Format. I am satisfied that the first four columns of this row (chromosome, start_position of feature, stop_position of feature, gene) are in BED format. Now i wish to structure the remaining two rows so that the complete row is in BED Details Format. 

BED Details Format involves the addition of two extra columns to the BED format so that the first column contains some ID, and the second column contains multiple pieces of information. My questions are:

1. For the creation of a BED Detail Format file,  do i have to keep the ID column at all? Can i not just have one additional column in addition to the columns required in BED format which would contain multiple pieces of information like the IDs. 

2. In the ID column, am i permitted to keep multiple IDs with a separator. For instance, DOI ID, PMID, OMIM ID, etc. or do i have to keep all these IDs in the column containing multiple pieces of information. When keeping an ID, i don't just want to give some ID but i also want to mention what kind of ID it is. For instance, DOI or PMID and so on. 

Regards

Vikram

[Matthew Speir]

Hello Vikram,

Thank you for your question about the bedDetail format. You are allowed
to keep multiple IDs in the ID column. These IDs can be separated by
spaces, commas, or nearly anything except a tab. The tab separator is
reserved for separating the columns themselves. If you intend to use the
bedDetail format, you should use the ID column as the Genome Browser
expects this column to be there.

You may also want to consider using the bigBed format,
http://genome.ucsc.edu/goldenPath/help/bigBed.html, for your data. The
bigBed format has a few advantages over the bed and bedDetail formats.
First, it is a compressed binary format, which means that the final
files are going to be smaller than your standard bedDetail files.
Second, you can use a custom AutoSql (.as) file to define as many extra
columns as you would like. This means that you can define DOI, OMIM,
etc. columns for your bigBed file. See "Example 3" on the bigBed format
description page,
http://genome.ucsc.edu/goldenPath/help/bigBed.html#Ex3, for more
information on creating bigBed files from your bedDetail file and a
custom .as file. You can download the bedToBigBed utility described on
that page from the appropriate directory for your system here:
http://hgdownload.soe.ucsc.edu/admin/exe/.

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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