If you read the bed format you know that the first base is at 0 and the end is not included in the range. So the first 100 bases of the genome look like: chrSomething 0 100
As a position it would be: chrSomething:1-100 So the region you are trying to lift is of size 0, and does not map to any chain, so it gets dumped into the "#Deleted in new" pile. I believe this is the line you want: chr22 297635 297636 rs132808775 0 + -Galt 10/6/2011 6:54 AM, LU Zen: > Hi, > > I have been getting different result from the liftover when using a BED or a > Genomic Coordinate Position file. For example, to convert the BtauMD3 to > Btau4; > > giving the following bed line: > chr22 297636 297636 rs132808775 0 + > returned this: > #Deleted in new > chr22 297636 297636 rs132808775 0 + > > but giving this: > chr22:297636-297636 > would successfully produce the conversion: > > chr22:1387-1387 > > As far as I can see, those that failed in the BED file are insertions with > chromstart equal chromend. So should I change all the chromstart in the BED > file to chromstart-1 during the liftover and then change them +1 after the > conversion? > > Thanks, > Zen > > ******************************************** > Zen H. Lu (PhD) > Bioinformatics Group > Division of Genetics& Genomics > The Roslin Institute > University of Edinburgh > Easter Bush > Midlothian EH25 9RG > Scotland UK > > Tel: ++ 44 131 651 9157 > E-mail: [email protected]<mailto:[email protected]> > ******************************************** > > > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336. > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
