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
