Can you please provide the bed files for the top 10,000 TFBS selected for the 377 TFs?
You provide bed files for the scATAC and DHS sites, but not the TF sites. I don't see those sites in the original Griffin GitHub either - only CTCF for the demo run.
from the READ ME:
-
Tissue-specific DNase 1 hypersensitivity sites (DHSs) were obtained from the ENCODE regulatory index to construct 16 tissue-specific open chromatin maps (https://www.meuleman.org/research/dhsindex/). The top 10,000 DHS summits from each tissue were selected on the basis of ranking by highest recurrence across experiments (‘numsamples’) and mean DHS signal (‘mean_signal’), marked in column called 'scores'.
-
19 tissue-specific open chromatin maps were generated from published single-cell transposase-accessible chromatin sequencing (scATAC-seq) data (http://catlas.org/humanenhancer). For open chromatin sites, the top 10,000 peaks were selected by peak scores marked in column called 'scores'.
-
Transcription-factor-binding sites (TFBSs) for 377 transcription factors were obtained from the Gene Transcription Regulation Database (GTRD), and the top 10,000 TFBSs were filtered on the basis of recurrence across experiments, as described in our previous study (https://doi.org/10.1038/s41467-023-36187-8). <-- APPEARS MISSING
Can you please provide the bed files for the top 10,000 TFBS selected for the 377 TFs?
You provide bed files for the scATAC and DHS sites, but not the TF sites. I don't see those sites in the original Griffin GitHub either - only CTCF for the demo run.
from the READ ME:
Tissue-specific DNase 1 hypersensitivity sites (DHSs) were obtained from the ENCODE regulatory index to construct 16 tissue-specific open chromatin maps (https://www.meuleman.org/research/dhsindex/). The top 10,000 DHS summits from each tissue were selected on the basis of ranking by highest recurrence across experiments (‘numsamples’) and mean DHS signal (‘mean_signal’), marked in column called 'scores'.
19 tissue-specific open chromatin maps were generated from published single-cell transposase-accessible chromatin sequencing (scATAC-seq) data (http://catlas.org/humanenhancer). For open chromatin sites, the top 10,000 peaks were selected by peak scores marked in column called 'scores'.
Transcription-factor-binding sites (TFBSs) for 377 transcription factors were obtained from the Gene Transcription Regulation Database (GTRD), and the top 10,000 TFBSs were filtered on the basis of recurrence across experiments, as described in our previous study (https://doi.org/10.1038/s41467-023-36187-8). <-- APPEARS MISSING