Closed BenSolomon closed 2 years ago
I have a similar question - I am using the following cisTarget databases: (1) hg38refseq-r80500bp_up_and_100bp_down_tss.mc9nr.feather (2) hg38refseq-r8010kb_up_and_down_tss.mc9nr.feather
I would like to understand how the scores from these are combined in pySCENIC.
I believe this comment in #334 may cover this question. When using multiple cisTarget databases, each module is pruned separately against each database, then later combined.
Apologies if this is a naive question, but if different PWM reflect the extent of the promoter sequence considered for possible TF targets, would that make a
500bp_up_and_100bp_down_tss
PWM a subset of a10kb_up_and_down_tss
PWM? In other words, would you expect to find any regulons enriched by a500bp_up_and_100bp_down_tss
PWM that wouldn't be enriched with a10kb_up_and_down_tss
PWM, given the later should also cover the +500 to -100bp region from the TSS sequence for each target?If the answer is no, I'm curious about part of the code in the tutorial for incorporating ChIP-seq tracks rather than motif sequences as PWMs. Specifically this segment:
This seems to utilize both
500bp_up_and_100bp_down_tss
and10kb_up_and_down_tss
PWMs at the same time. My two questions related to this are:1) What is happening when multiple PWMs are specified? How are the scores for identical motif/track x TF target values between the two matrices combined?
2) As above, will the combination of the of the
500bp_up_and_100bp_down_tss
and10kb_up_and_down_tss
PWMs result in any enriched targets that the10kb_up_and_down_tss
PWM would not also enrich on its own?Thank you!