Tag: FRiP

RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…

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low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

Hi. I’m doing ATAC-seq analysis of colon tissue. I analyzed 1)QC -> 2)Mapping -> 3)Post alignment processing(remove mt reads, duplicated reads, multi-mapped reads) -> 4)Peak calling order. However, as a result of calculating FRiP after peak calling using MACS2, the FRiP score was too low. No major problems were found…

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Normalization and differential analysis in ATAC-seq data

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

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low number of significant peaks for one contrast

I am using Diffbind to call differential peaks on an ATAC seq dataset of four conditions (AW, BW, B, and C), and each condition has 2 replicates. One of my replicates (BW2) has low quality (low number of peaks detected by MACS2 compared to the other replicate, and low FRiP)….

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