How to do multiz alignment locally
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15 days ago
Santex • 0

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.

axtChain lastz multiz • 159 views
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