engreitzlab / abc-gwas-paper Goto Github PK

Hello,
based on your Genome-wide enhancer maps link risk variants to disease genes, you used ABC model to prediect the taget genes of fine-mapped GWAS varints, not all SNPs. Do I use ABC model to identify the target genes of all GWAS varaints?

Dear authors @engreitz @jnasser3 @kmualim ,

Thanks for your beautiful work.

The code provided in ABC-Max file produce CellTypeEnrichment.IBD.pdf is totally different with the CellTypeEnrichment.IBD.pdf in ABC-max/out file.And these two pictures are different from the Fig1.a in the paper [ https://www.nature.com/articles/s41586-021-03446-x ] .How to get the CellTypeEnrichment.IBD.pdf?

Thanks in advanced.

Dear authors @engreitz @jnasser3 @charlesfulco,

I am following your article 'Genome-wide enhancer maps link risk variants to disease genes' published on Nature in 2021, and encountered some problems when processing data.

The online Supplementary Information describes Supplementary Table 3 as a zipped file contains CRISPRi-FlowFISH data: data per guide. And the full legends in the Supplementary PDF say Supplementary Table 3 contains effects of CRISPRi perturbations to candidate regulatory elements, with each row representing one gRNA tested for one gene in one cell type.

However, Supplementary Table 3 is provided in .txt format and only contains 'chr', 'start', 'end', 'GuideSequenceMinusG', 'IsNegativeControl', 'Gene', 'ScreenRep', 'count', 'Bin' and 'PCRRep' 10 columns, missing the cell type information. And the values in the'IsNegativeControl' column are all False.

I think an error occurred while uploading supplementary materials. Can you send me the correct document?

Looking forward to your reply.

Thank you.