Hello, If the input BED file contains strand, the results from liftOver will also include strand. Strand is the 6th field of a BED file. http://genome.ucsc.edu/FAQ/FAQformat#format1
As an example, I used the default location for Rhesus Jan. 2006 and created a BED6 file: chr7 58999504 59100350 1 2 - Using liftOver with default parameters for cross-species lifts (minMatch = 0.1 and multiple=Y), this is the result versus Human GRCh37: chr15 80174150 80279565 1 2 - (Note that I filled in the columns 4 & 5 with mock data, you can of course make this informative if you want. Please try this method and see if it works for you, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Perdeep Mehta" <[email protected]> wrote: > From: "Perdeep Mehta" <[email protected]> > To: [email protected] > Sent: Wednesday, January 13, 2010 2:59:18 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] liftover across species with strand orientation info > > Hi, > > I'm trying to liftover the coordinates for several genomic locations > on the Rhesus genome over to Human genome. The most simplest I have > learned is to use BED format to provide chr, start, and end location. > It is working and I have no problem mapping Rhesus coordinates > correctly to Human. The question I have though, is there a way that I > can get strand orientation on the Human genome without going through > BLAT? > > The liftOver can have orientation information if I use psl formatted > BLAT output file as input. I want to skip BLAT since we have reads > that can be between 15-20 bp long. > > Thank you for any suggestion. > perdeep > > > ________________________________ > Email Disclaimer: www.stjude.org/emaildisclaimer > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
