CrossMap Genome Coordinate Converter, Start Location is further than End location Problem
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8.3 years ago
morovatunc ▴ 550


We have two data which their reference genomes are different. My core data is referenced to hg19 where this one single chip seq bed file is allingned to hg18. I would like to compare this new file with my existing data to make observe the correlation.

Referring to Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api) thread. I took cross map as a tool based on the reviews under the question post. But When I converted the data, It generated multiple errors that start location of the peak appears to be further 1 base than the end location. This one base is consistent for all the errors. However, Crossmap did not give any errors regarding this error. Moreover, out of these error lines, my other peak coordinates seems to be transformed.

Therefore I have a few questions:

  1. Is my alignment correct for rest of the peak coordinates, even though I get this error? This error seems to be an analogues of the frame shift. I believe this error seems unimportant but it might have messed up my whole conversion. So I don't trust it?
  2. I can remove those lines manually by hand no problem. But is there a method to do that? (this question is true in the case of the whole conversion right.)
  3. Could you discuss a little bit?

Thank you for your help.


hg18 crossmap genome-coordinates hg19 • 2.1k views

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