RNAseq and ChIPseq integration
Hi all,
I have two replicates of RNAseq data for four different condition (one unstimulated and three different stimulation) with and without a transcription factor(TF) Knock down and ChIPseq data of this factor in all these four condition. I would like to study the effect of stimulation, knock-down and TF binding. what approach/analysis i should take to address my question. I know this is very broad question, any suggestion/guidance will be appreciated.
Note: I have already analyzed RNASeq data and ChIPseq data and have expression and binding information with me.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
merging bam file
written by qudrat.nii •
-
DiffBind - Comparing normalization/background methods - how to create a heatmap (as in 7.5)?
written by bertb •
-
Quantification of acetylation enriched regions at transcription factor binding sites (WT vs KO)
written by massimofaggiani •
-
Log2 fold change correlation for ChIP seq data - do I need a FDR cut off?
written by brisbio •
-
General Enhancer Questions (Methylation Patterns, ect.)
written by gtasource
-
How should analyze if a Transcription factor significant in one condition vs. another using centipe…
written by zhaolin20042008 •
-
Correlation of TF Binding with expression data
written by Prakash
-
What is the best method ChIPseq differential binding analysis?
written by biopat •
-
Identify genes near occurrences of a TF binding sequence
written by codybj •
-
Can I use AME - Analysis of Motif Enrichment - for RNA-Seq data?
written by Chris Gene
A broad question deserves a broad answer. Venn diagrams and heatmaps. : D
Okay, that was a bit snarky. One thing you could consider to start with is the overlap between differentially regulated genes and genes with ChIP-seq peaks... And whether that overlap is more than you would expect by chance.