usage of --slocal and --llocal

[emancera]

I am trying to run macs so that it does NOT consider the background lambda (λBG) when getting the maximum lambda to calculate the local lambda. I just want to use the 1kb, 5kb and 10kb window lambdas when calculating the local lambda. Is this possible using --slocal and --llocal?

From the explanation of --slocal and --llocal it is not clear whether when you specify these parameter the background lambda (λBG) is still considered when calculating the local lambda.

Thanks for the help,

E

[taoliu]

You can do so by utilizing the subcommands in MACS2. I have updated MACS2 codes to enable certain functions in subcommands (e8da469). And I am currently updating the wiki page: https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands

[taoliu]

Hi Eugenio, please check the wiki page https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands Especially the section about how to build local bias track.

[emancera]

Thank you very much again, I will have a look.

Eugenio

On Fri, Feb 12, 2016 at 1:52 PM, Tao Liu (τν) notifications@github.com wrote:

Hi Eugenio, please check the wiki page https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands Especially the section about how to build local bias track.

— Reply to this email directly or view it on GitHub https://github.com/taoliu/MACS/issues/111#issuecomment-183501514.

[taoliu]

@emancera Don't forget to update your MACS2 to the current version on github -- you also need cython to install from the source codes on github. Some of the functions mentioned in the wiki page are not available in older version. Will release a MACS2 package on PyPI website in days.