Hello Mikhail:
What happens when you just lift those first 4 lines alone? Could you
also confirm whether you're using web-based or the stand-alone tool?
I am lifting your data both via the website and from the commandline,
and I do not see the "+" --> "1" conversion.
Kayla Smith
UCSC Genome Bioinformatics Group
Mikhail Bilenky wrote:
> 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
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
