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zhoulab / p53-chip-seq-data

Basic machine learning on genomic data
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User input for mast file #9

Closed varsh1090 closed 6 years ago

varsh1090 commented 7 years ago

To be able to use a different mast_out file to generate P53_match scores column of mastertable

victorlin commented 7 years ago

The pipeline is now set up using a Makefile. You can generate the melted master table simply using the command:

make results/ChIP_master_table.txt

and I added support for the two pivoted formats:

make results/ChIP_master_table_fe.txt
make results/ChIP_master_table_macs.txt

If you want to change any of the input files, you can edit the Makefile directly. I've made variables in that file so it's easier to keep track of and modify the pipeline.

(side note: you must be in the directory /ufrc/zhou/share/projects/bioinformatics/p53-chip-seq-plots, have modules homer, bedtools, python, and R, loaded, and have the virtualenv activated. I've created a script to do all that: simply go to the directory and run source hpc_set_env.)

victorlin commented 6 years ago

P53match_score column is not used anymore.

On a related note, data/MAST/ directory is used in binding prediction datafile.