Question: How do I use Diffbind as a complete beginner?
0
gravatar for AA
23 months ago by
AA0
AA0 wrote:

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?

chip-seq diffbind • 2.0k views
ADD COMMENTlink modified 23 months ago by igor7.6k • written 23 months ago by AA0
2
gravatar for igor
23 months ago by
igor7.6k
United States
igor7.6k wrote:

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:

ADD COMMENTlink written 23 months ago by igor7.6k
1

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

ADD REPLYlink modified 23 months ago • written 23 months ago by YaGalbi1.4k
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