[Genome] BED formatted files for liftOver

[Heather Trumbower]

Sen:

You need to supply some sort of default value for each column.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Sun, 7 Jan 2007, Tay Sen Kwan wrote:

> Hello,
>
> I am trying to use the liftOver tool in batch mode using input files in BED
> format.  This format has 3 mandatory fields and 9 optional fields.  For the
> optional fields, I would like to know if the field is not used, what is the
> procedure ? i.e. I understand the fields need to be separated by 'space', do
> I have to put in a dummy values to maintain the total number of fields or I
> only have to put in values for fields that are actually used.  For the
> latter, how does liftOver knows how to assign the values to the correct
> fields ?
>
> e.g. for the optional fields, I only need the name, strand, blockCount,
> blockSizes and BlockStarts - should a typical line be:
>
> chr1      1000     2000     hit1       +          0          2
> 30,200  1000,1100
>
> I understand that the '0' before blockCount is required as the 'reserved'
> value.  Or do I have to use:
>
> chr1      1000     2000     hit1       900       +          1000     2000
> 0          2          30,200  1000,1100
>
> ie 900, 1000, 2000 are just dummy fillers.
>
>
> Regards,
>
> Sen Kwan
>
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