[Genome] BED formatted files for liftOver

[Tay Sen Kwan]

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