[Genome] correction of chunk coordinates in blastz alignments
Wang JianLi
jlwang at imcb.a-star.edu.sg
Wed Mar 5 22:52:08 PST 2008
Hi All,
I split human genomic sequences into chunks with size 10M, and overlap size 10K, and run blastz to align each chunk with another genome. Then I have a number of .lav files after the blastz. I am not sure how I can piece them together, to correct the coordicates of the sequence chunks. As in each chunk, the sequence coordinate will start from 1, but in the original chromosome sequence, this coordinate should be adjusted by the size of chunks and overlap region.
I read that blastz-normalizeLav written by Scott Schwartz can do that. Does anybody know where to get that script?
Thank you.
Regards,
J.L
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