ATAC-Seq Analysis - only peak counts and peak loci files available
0
0
Entering edit mode
2.3 years ago

I have a file with peak counts (2 groups - treated and control, 3 replicates each) and a bed file with peak loci. I don't have access to any prior files i.e. fastq and BAM files, so cannot complete the full workflow from scratch. Could anyone advise on how I could perform differential accessibility analysis only with this data?

Thank you

ChIP-Seq sequencing • 1.3k views
ADD COMMENT
0
Entering edit mode

With peak counts I assume a count matrix with rows = peak regions of both conditions and columns = the raw counts for every sample? If so, you can feed that into any downstream franework you like, e.g. edgeR, DESeq2.

ADD REPLY
0
Entering edit mode

Hello all, I’m doing ATAC seq differential peak analysis. I only have a file with the peaks counts from 2 groups with 3 replicates each, and the peak loci in a bed file. I run the differential analysis using the peak counts file in DESeq2 and have a list of DE peaks. I would like to know how to annotate those regions to gene names using the peak loci in the bed file. From the peak count file I have a column with peak IDs in the format 1:181674-181967; while in the bed file I have 3 columns: chr number, start and end. How can I merge those files and identify the gene name annotations? Thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 1529 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6