repli-seq analysis pipeline

Question

[2nelly]

Hi all,

https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/repli-seq.html

Does anybody know a good pipeline to analyze repli-seq data (please see the link above) in order to find origins peaks? I know that most callers are optimized for chip-seq. Do you think MACS is good enough to call this type of peaks?

thank you in advance!

[Lila M]

Hi! Did you find the way to analyze the data? Im in the same situation!

[trausch]

I did create a very basic Repli-Seq analysis workflow a while ago.

[Lila M]

Thank you very much! One more thing, how is the normalization doing?

[trausch]

As far as I remember I used the normalization from this paper.

[Lila M]

But is somehow normalised to the Input or independent of it? Thanks!

[trausch]

It depends on the input BAMs.

[Lila M]

what do you mean? can you please be more specific? Thanks!