search

nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
177 stars 144 forks source link

Normalisation of bigwig files #357

Open alhh507 opened 11 months ago

alhh507 commented 11 months ago

Description of feature

Hi there,

Firstly, thank you nf-core team for the development of this chip-seq pipleine. I have used it successfully multiple times, I LOVE IT.

I was just wondering about the specifics of the normalisation procedure.

You write on the pipeline overview page "Create normalised bigWig files scaled to 1 million mapped reads"

Does this mean that the generated bigwig files are just scaled to reads per million - or are these resulting bigwig files also normlaised to input?

If they are normalised to input are they IP-input or IP/input? Also, if they are normalised to input then is there a way to circumvent this?

Thanks and all the best,

Alex