Closed jasondanic closed 11 months ago
Hello,
Yes the sign indicates up-regulation or down-regulation with respect to the ref allele.
I am not aware of the source you are pointing to. Maybe you can share the url directly? SNP data need not be in the peak necessarily, but you can imagine that a log fold change of x more reliable in peaks than in background. The max percentile column in variant-scorer captures this idea. I recommend posting in the variant scorer package GitHub for further clarification - - https://github.com/kundajelab/variant-scorer.
Thank you, Anu
Hi,
I got several questions about understanding the results when using variant_scoring.py from https://github.com/kundajelab/variant-scorer. The main question arises from the logfc.mean, which is composed of both negative and positive values. Given that these results differ between alternate allele and reference allele predictions, can I interpret positive values as indicating up-regulation in accessibility caused by the mutation, and vice versa? This also raises another question regarding the input of SNP data: does the SNP data need to be within the scATAC-seq peak regions of a specific cell type or just all of it? Based on the method described in this articlehttps://doi.org/10.1016/j.cell.2022.11.028, it appears that thresholding the mutation impact scores involves selecting mutations from peak regions (as shown in the screenshot below).
Thanks.