Kayla, Thanks for the reply. I was using the web-based tool.
Yes, just for lines don't create a problem. It happens with a file that has ~40K lines. Misha -----Original Message----- From: Kayla Smith [mailto:[EMAIL PROTECTED] Sent: Thursday, October 30, 2008 3:18 PM To: Mikhail Bilenky Cc: [email protected] Subject: Re: [Genome] Lifting tool 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
