I have been using UCSC's liftover utility with worms closely related to C. elegans. The genome version of C. elegans that I am using is ce10. http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans

I encountered a few problems.

1. What is the difference between ce10.caePb3.all.chain.gz and ce10ToCaePb3.over.chain.gz? These files can be found in the following places: here and here.

2. What are the *.net.gz files? For example ce10.caePb3.net.gz ?

3. My ultimate goal is to take coordinates from C. elegans, map these coordinates to another nematode and then extract the sequences. When I run liftover:

liftOver input.bed ce10.caePb3.all.chain lifted.bed deleted.bed

I get output that looks like this:

Scfld02_1087 4253 4254

Next I could use a tool like fastaFromBed in the bedtools package if I could find the right FASTA file. How can I match the .over.chain/.all.chain files with the FASTA file used to create it?