I'm trying to do Multiz Alignment locally with Human, Mouse, Chick, Alligator, Xenopus, Spotted gar, Sea lamprey. I wrote down the overall flow that I understand so far. I want to confirm it, so please correct it when it's not. I'm a windows user working on Ubuntu.
1.) Get the target sequence in ".fasta" format and ".2bit" format.
2.) Run lastz in all the sequences.
ex.) if I use only human, mouse, and chick.
lastz human.fasta mouse.fasta --output=human_mouse.axt
lastz human.fasta chick.fasta --output=human_chick.axt
lastz mouse.fasta chick.fasta --output=mouse_chick.axt
3.) Run axtChain in all axt output files.
ex.) if I use only human, mouse, and chick.
axtChain -linearGap=loose human_mouse.axt human.2bit mouse.2bit human_mouse.chain
axtChain -linearGap=loose human_chick.axt human.2bit chick.2bit human_chick.chain
axtChain -linearGap=loose mouse_chick.axt mouse.2bit chick.2bit mouse_chick.chain
4.) Run multiz in all chain output files.
ex.) if I use only human, mouse, and chick.
multiz human_mouse.chain human_chick.chain mouse_chick.chain > final.maf
QUESTION a.) Now, I finished axtChain. chatGPT tells me to do chainPreNet and chainNet before moving on to multiz when the species are highly divergent.
b.) I also want to confirm each command. I couldn't find an instruction, so if it is possible, please tell me the URLs that I can check and study.
c.) after running the multiz locally, I want to visualize it on the UCSC genome browser. Are there any useful tools to do it? Any other recommendations for visualization?
Please help me out with those problems.
