DiffBind analysis with ENCODE data using R and .bed/.bam files

Question

[stalo.lili]

Hi everyone, I’m new to ChIP-seq and DiffBind, and I’m trying to analyze transcription factor binding using ENCODE project data. I have .bed and .bam files for 20 individuals, comparing state 1 vs state 4 of a disease. I’ve found start from FASTQ files and involve full alignment and peak calling pipelines, but since I already have .bam and .bed files from ENCODE, I’m not sure how to proceed directly from this point in R using DiffBind. I got confused because most examples assume FASTQ-level input, which I won’t be using at this stage (though I’ll be doing RNA-seq later). Could someone please guide me through the workflow or point me to a resource that starts with .bed/.bam files for differential binding analysis using DiffBind? Thanks so much in advance!

Answer 1

[Aspire]

most examples assume FASTQ-level input

Perhaps the reason for this impression is looking in ENCODE pipelines&workflows. But take a look at the DiffBind vignette. Also see a tutorial on DiffBind