I have .wig files for H3K9me3 ChIP and corresponding input samples. These are not library normalised and when uploaded on IGV, displays the absolute read …

I have a bed file with genomic coordinates, I used bedtools multicov to get the reads mapped to each of the regions. I have to …

I know the way MACS2 uses Poisson distribution to find the p value for the enrichment of a signal peak(observed) as compared to the local …

Hello all, I want to compare chip-seq signals of polymerase1 and polymerase3 over few bed coordinates but I guess I must be normalizing these chip-seq …

Hi all, Sorry in advance if this has been asked other places: we plotted heatmaps of H3K4me3 ChIP-seq signal with our interested regions in different …

Hello, I have some chip-seq data for three different conditions for which I have plotted RPKM normalized counts around features of interest using deeptools. The …

I processed my ChIP-seq and ATAC samples using the ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2 and https://github.com/ENCODE-DCC/atac-seq-pipeline). These pipelines gives outputs such as aligned bam files, bigwig files …

Hi everyone, I need to identify which genes in my histone ChIP-seq experiment have greater signal for chip than for input (enrichment). I have made …

Hi all, It is very common to perform clustering analysis when plotting ChIP-seq. signal as a heatmap (e.g. around TSS) for finding regions having similar …

Hi all, Although the Input control is commonly used for in ChIP-seq. analysis (e.g. for normalization, as background for peak calling), it seems hard to …