Tag: FRiP

CHiP-Seq Questions

CHiP-Seq Questions 0 Hello, New to chip-seq analysis so I apologize in advance for the questions. Currently using diffbind. I see that the interval number for one of the replicates out of the 3 is very high compared to the other 2 replicates. FRiP score across samples is also lower…

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DiffBind missing peaks and FRiP

DiffBind missing peaks and FRiP 2 I noticed that when I first read in my sample sheet, I get a DBA object with 1226 sites (consensus peaks), yet after running dba.count() on this same object, it is down to 1188 sites. I did not apply any blacklists/greylists. Also, the FRiP…

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Diffbind dba.count doesn’t give FRiP score

Diffbind dba.count doesn’t give FRiP score 1 Hi I am completely new to DiffBind, R and programming in general. I want to use diffbind to analyze peaks called with macs2. When I use dba.count(), I can not get FRiP score at all. I googled this question, but didn’t work. Here…

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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I…

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New technology maps where and how cells read their genome

Design and evaluation of spatial epigenome–transcriptome cosequencing with E13 mouse embryo. a, Schematic workflow. b, Comparison of number of unique fragments and fraction of reads in peaks (FRiP) in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. c, Gene and UMI count distribution in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. Number of pixels in…

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How to quantify the reads of each peak for ChIP-seq data?

How to quantify the reads of each peak for ChIP-seq data? 1 Hello I can quantify the total reads of all the peaks in a peak file using DiffBind, the tamoxifen.csv: SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller BT4741 BT474 ER Resistant Full-Media 1 reads/Chr18_BT474_ER_1.bam BT474c…

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Telomere-to-mitochondria signalling by ZBP1 mediates replicative crisis

Cell culture IMR90 (CCL-186) and WI38 (AG06814-N) fibroblasts were purchased from ATCC and the Coriell Institute for Medical Research, respectively. IMR90 and WI38 fibroblasts were grown under 7.5% CO2 and 3% O2 in GlutaMax-DMEM (Gibco, 10569-010) supplemented with 0.1 mM non-essential amino acids (Corning, 25-025-Cl) and 15% fetal bovine serum (VWR/Seradigm,…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

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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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