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CL-CHEN-Lab / OK-Seq

R package for the analysis of OK-Seq data to study DNA replication fork directionality: from count matrices, RFD calculation to inititation/termination zone calling.
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Reg: Combining replicate regions and regions flipping between presumed IZs or TZs #4

Open harish0201 opened 1 year ago

harish0201 commented 1 year ago

Hi!

We are currently analyzing a few TrAEL-seq data-sets using OK-Seq package here. We had a few questions regarding combining the "peaky" or forking regions identified from replicates.

  1. Do you have any particular recommendation for identifying/combining the peaks between the replicated samples?

What would be a good distance for combining nearby TZs, IZs etc?

For example:

Replicate A:

chr1 1000 1500 chr1 2000 2800

Replicate B:

chr1 1100 1400 chr1 2200 3000

Should we take the entire span like so:

chr1 1000 1500 chr1 2000 3000

or just the overlapped region between the two, like so:

chr1 1100 1400 chr1 2200 2800

  1. While looking at the regions called by OKSeqHMM, we see multiple blips. image

For example, see the 5078logy TZ and IZ tracks at the bottom of the image, while its replicate 5078logx doesn't seem to have a lot of the blips from TZ to IZ. We are a bit confused about these blips since some of these occur right around/on top of ARS regions in yeast, but have no specific pattern

Would there be a particular reason for these blips occurring? Should we consolidate these TZs interspersed with IZs in a singular region?

I can check with the PI of the project to see if they can allow sharing the trackhub for the particular segment above, but could I have your email address so that we can send these datasets confidentially? But any help in this particular issue would be really appreciated!

Regards, Harish

CL-CHEN-Lab commented 1 year ago

Hi Harish, you can sent me an email (chunlong.chen@curie.fr) for a further discussion.