UCSC LiftOver questions

[geneart]

Hi Folks,
Anyone familiar with using UCSC LiftOver option ? Althoguh it should convert one track of sequences into another tracks taking into account the + and - orientations and multiple files , I am not able to do it !!!! Can we just upload the".txt " file after having all sequences in "chr 12345 5678 xxx "format?
Any help will be appreciated !!!!

[Heisman]

I think your format needs to be like:

chr4:384-4920

[holywoool]

usage:
liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and maybe eventually others with the appropriate flags below.

I had change the input into BED format and can run liftOver successfully.
BED format requires 6 columnssee ucsc annotation database:http://genome.ucsc.edu/goldenPath/gb...ptionsOld.html)
chr19 63762364 63777976 NR_027334 0 +

[geneart]

The format I had worked for my +ve sequences but when I try to upload my file with reverse seq I keep getting error. Any help in uploading this onto the LiftOver and successfully getting the reverse strands to work? Thanks in advance.

[geneart]

I did flip the start and end pos in my reverse file.............still there is an error

[dpryan]

It would help if you mentioned what the actual error is. Also, show us a few lines from the file that's producing the error.