Hello, Craig. Unfortunately, the liftOver tool does not have a method of one-to-one mapping like you describe. There is, however, a way to "cheat" to obtain the results you're looking for.
The following example assumes you have a list of your coordinates in BED6 format in a file called original.bed (see the BED format page at http://genome.ucsc.edu/FAQ/FAQformat#format1). Run the following UNIX shell command: awk 'BEGIN{OFS="\t";} \ {print $1, $2, $3, \ $4 "|" $1 "|" $2 "|" $3, \ $5, $6;}' \ original.bed > forLiftOver.bed This concatenates your original coordinates and inserts them into the fourth column of the BED6 output file. You can then feed the output file into the liftOver tool and see your original coordinates alongside the liftOver coordinates. From your results, you can split the concatenated original coordinates back into their own columns if desired. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Benson, Craig C Sent: Wednesday, February 15, 2012 9:41 AM To: '[email protected]' Subject: [Genome] liftOver Does the liftOver utility give a one-to-one mapping of the coordinates that are being "lifted" or aligned from one genome to the other? For instance, I have nearly 80,000 sequences that I am lifting to another genome. Is there a way to have the output of liftOver be a listing of the one-to-one mapping? Thanks, Craig _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
