Hi everyone, I have a problem here, I need some help with a .chain file. I need to convert an old version of a genome to another. Does anybody knows how to read that kind of file? Thanks a lot.
Heads up! This is a static archive of our support site. Please go to help.galaxyproject.org if you want to reach the Galaxy community. If you want to search this archive visit the Galaxy Hub search
Question: Reading files .CHAIN?
0
Marcos Lancia • 10 wrote:
ADD COMMENT
• link
•
modified 18 months ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
18 months ago by
Marcos Lancia • 10
1
Jennifer Hillman Jackson ♦ 25k wrote:
Hello,
Do you mean that you want to convert the coordinates of features based on an older version of a genome to those of a newer version of the same genome? (Or the reverse?). And possibly extract fasta genome sequence for those features?
If so, the tool LifeOver can be used. It is available in Galaxy in the tool panel. Not all genomes are supported but most are or can be added if they are sourced from UCSC.
This tool is based on the Batch Coordinate Conversion utility from UCSC and is also available for use at their website.
If your genome-to-genome mapping is not available in Galaxy yet, but the chain/liftover files from the Conservation track at UCSC exists, let me know and we can help with the request.
Thanks! Jen, Galaxy team
Please log in to add an answer.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 181 users visited in the last hour