How do I use Diffbind as a complete beginner?

Question

[AA]

I am very new to bioinformatic and genomic analyses. So far I have learned how to do the basic ChIP-seq workflow in Galaxy, including using Bowtie2 to map reads to the genome, MACS2 to call peaks, and doing motif searching.

Now I'd like to learn how to identify sites that are deferentially bound between two sample groups. I've read through the Bioconductor manual for Diffbind (http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf) but I do not understand much beyond the Introduction section.

I've installed R and RStudio, but am not knowledgeable in programming languages. I'm wondering how much I need to learn to be able to perform Diffbind on my ChIP-seq datasets.

Are there any Diffbind tutorials/guides for complete newbs?

[Aspire]

Here

Answer 1

[igor]

The DiffBind vignette you linked to is probably the best guide for DiffBind.

If you have trouble understanding it, I think what you are looking for is a general R tutorial, such as:

• https://www.datacamp.com/courses/free-introduction-to-r
• http://tryr.codeschool.com/

[BioinfGuru]

also make sure you have replicates... apart from the fact that your results will be very questionable if you dont, without replicates diffbind will be a nightmare for you