How to use moccasin for MAJIQ

[Swethaa NG]

Dear team,

I have BAM and BAM.BAI files of samples run in different batches. I ran majiq build for them, so these are uncorrected .majiq files. Now, I want to run moccasin to generate new batch corrected .majiq files. I made a model matrix stating the batches and filenames.

Should I have a junction count matrix too? 

I cloned the moccasin files to my directory. Should I add or change something in the moccasin.py file? 

I am unsure on what to do next. Please guide?

Kind regards,

Swethaa

[San Jewell]

Hi Swethaa,

The program readme for moccasin can be found here: https://bitbucket.org/biociphers/moccasin/src/master/ , note specifically the "program call" section.

Basically, you'll want to run something like:

$ python moccasin.py <model_matrix> <majiq_build_dir> <out_dir> <one or more confounding factors>

Note that there are also many other options available in the program call which are documented there.

Please let me know if this instruction makes sense.

Thanks!

-San

[Swethaa NG]

Hi,

Thanks a lot for your help! :)

Great!! Yes! I will check that and work it out. Thanks!

Kind regards,

Swethaa