Hi there,
It is a minor observation, but still I'd like to mention it.
I am using the UCSC batch lifting tool, trying to lift genomic
coordinates defined in mm9 into coordinates in mm8
My input BED file looks like that
chr3 64494582 64495004 39139 . -
chr3 65197243 65199364 39141 . +
chr3 67423718 67424650 39146 . -
chr3 68212034 68212402 39147 . +
...
and it has ~40K lines
The output I am getting looks like
chr3 64778589 64779011 39139 . -
chr3 65481250 65483371 39141 . 1
chr3 67707725 67708657 39146 . -
chr3 68496041 68496409 39147 . 1
...
and it is not in the BED format anymore (all '+' --> '1')
I checked that this change is consistent.
Also it looks when converting smaller files (<100 lines)
everything works ok ('+' remains '+' after lifting).
Misha
Misha Bilenky [EMAIL PROTECTED] <BLOCKED::mailto:[EMAIL PROTECTED]>
Gene Regulation (Informatics), BC Genome Sciences Centre
(604) 877-6000 ext 5408
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
