I am new in ATAC analysis.
I have a problem about how to transfer ATAC peak to gene symbol.
Here is the ATAC-seq: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3271041
GSM3271041_ATAC_sciCAR_A549_peak.txt.gz file contains five columns :
(id, peak, chr, start, end). What I am doing is to use
bedtools to transfer locations in chromosome to get gene symbols.
Here is an example from
id,peak,chr,start,end 9,1-68591-69091,1,68591,69091 10,1-91105-91605,1,91105,91605
I use bedtools to get the gene symbol of
id=9 , that is
I want to use these ''symbol-transfered'' ATAC-seq to integrate with RNA-seq which has gene symbols alreadly.
Am I right to do so ?