Working With Liftover Of Nematodes
0
0
Entering edit mode
10.2 years ago
Frank • 0

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?

liftover • 2.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6