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Welcome to the chrombpnet wiki!

TODO for chrombpnet wiki -

Preprocessing -

(1) Need to change pysam to pyfaidx to load fasta files - for consistency (2) Add pwm check and abort further run if this check fails (2) add support to do bigwig generation from fragments (3) Add docker images to install ucsc_tools too

GC-matched negatives

(1) Provide instructions on how to build exclusion bed for chrombpnet

Modisco -

(1) Finish documentation with the help of Soumya. What is missing (1) db for tomtom matches - how to get this (2) remove redundancy

Marginal Footprinting -

(1) Use average counts instead of average probability