Closed anapkut closed 4 months ago
promoter_activity_quantile_cutoff 0.3
is the one we use. expression_cutoff
is for when gene expression data is provided (which isn't something supported in the codebase as of now).hic_contact
column to see the score directly computed from your data. hic_contact_pl_scaled_adj
is the actual value used for contact, which incorporates some powerlaw adjustments.I would not recommend using the HiChIP data at this time — we have not developed the codebase to enable this. I suggest running ABC using just your ATAC and H3K27ac data Best, Jesse
On Wed, Mar 20, 2024 at 11:54 AM Anthony Tan @.***> wrote:
- promoter_activity_quantile_cutoff 0.3 is the one we use. expression_cutoff is for when gene expression data is provided (which isn't something supported in the codebase as of now).
- I would debug by looking at the EnhancerPredictionsAllPutative file and locating the E-G pairs that match your HiChIP data. You can look at the hic_contact column to see the score directly computed from your data. hic_contact_pl_scaled_adj is the actual value used for contact, which incorporates some powerlaw adjustments.
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Dear authors,
I am trying to run the ABC model using publicly available ATACseq, H3K27ac, H3K27ac HiChIP and my own expression data, but am running into a lot of issues and was wondering if you could help me. I have listed my questions below:
Thank you very much!
Best,
Ana Patricia Kutschat