Dear UCSC genome browser scientist,
I have a question in mapping the genomic coordinates between two close
species using liftOver tool.
I am trying to do a whole genome alignment between two yeast strains.
I have done the following.
1) collect the chromosomes of the two yeasts.
2) use blastz to align the two sets of chromosomes and obtain the
alignments in lav format
3) convert lav into axt using lavToAxt
4) thread the aligned segments into chains using axtChain
5) do Net procedure using chainNet
I obtained the final alignment in net format. What I want eventually
is to map the coordinate in one genome to the other. I learned that
lifeOver tool can do this task, can it not? I ran into some troubles
using the liftOver tool. Typing "liftOver" in my terminal showed me
that it requires files in BED format. Do you know if there is a tool
to create such a file? All I have now are the chromosomes in fasta
format. Another question is that one of the argument is in chain
format, I am wondering why it does not take the alignment in net format?
Appreciate your help!
Sincerely yours
Tsunglin Liu
Postdoctoral Researcher
Biodiversity Research Center,
Academia Sinica, Taiwan.
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
