# ATAC peak anatations

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

The 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 GSM3271041_ATAC_sciCAR_A549_peak.txt.gz

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 OR4F5.

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 ?

• Annotating each with with the nearest gene(s) is a more specific question, that's great. Elsewhere on 10X's site you can see a description of their annotation process. Essentially, if you get a list of genes in a BED file, you can use bedtools closest with your peak list to find the nearest genes. The will usually work as a first pass for most applications, but like I said above, it will highly depend on your specific biological question. May 9 at 19:25