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stjude-biohackathon / CRCminer

MIT License
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Implement PWM scanning. #4

Open j-andrews7 opened 1 year ago

j-andrews7 commented 1 year ago

This will require limiting to subpeaks (either ATAC/DNase (preferred) or H3K27ac constituent peaks) in (super)enhancer files to search for motifs that meet the user-specified threshold (FDR, FNR, log-odds score, etc), see #8.

I think the simplest approach for this is the pymemesuite implementation of FIMO, the developer of which very kindly also implemented the fasta-get-markov functionality of the MEME suite for us!

This would require no installation of system dependencies (like the MEME suite).

An alternative is the biopython motif scanning module, which is I believe more computationally intensive to come up with reasonable thresholds.

j-andrews7 commented 4 months ago

Actually use lightmotif for this instead, as it's much more performant.