Liftover Of An Entire Genome

Question

[KCC]

How do I do liftover from the worm genomes ce6 to ce10? I want to lift a whole wiggle or bedgraph file, not just a bed or gff3 file.

I will settle for any information on what sections map to which other sections on a genomic level. I can write the translation program myself if needed.

EDIT: Would it work to just make a bed file with each nucleotide listed like this:

chr 0 1 ... chr 1 2 ... chr 2 3 ...

and so on ... and run the standard liftOver program on that?

Answer 1

[Pierre Lindenbaum]

All the mapping from one region/build to another is already contained in the liftOver files. So I suppose you could parse and use those files to compute the whole transformation.

http://hgdownload.cse.ucsc.edu/goldenPath/ce6/liftOver/

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/ce6/liftOver/ce6ToCe10.over.chain.gz" | gunzip -c | more
chain 1420079490 chrI 15072421 + 0 15072421 chrI 15072423 + 0 15072423 5
221369    0    1
10668    1    0
510810    0    1
3441789    1    0
3353183    0    1
2898637    1    0
1086017    0    1
3102274    0    1
447671

see http://genome.ucsc.edu/goldenPath/help/chain.html for the "chain format":

The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense. (...)

[KCC]

Thanks, this was what I needed. Just completed the parser.