FRiPs calculation without IgG control

[MatteoFiumara]

Hi there,
Thank you very much for the amazing tutorial. I have a question regarding FRiPs calculation. In the tutorial you wrote: "We calculate the fraction of reads in peaks (FRiPs) as a measure of signal-to-noise, and contrast it to FRiPs in the IgG control dataset for illustration. Although sequencing depths for CUT&Tag are typically only 1-5 million reads, the low background of the method results in high FRiP scores. "
However, I don't really understand what you mean here by "contrast it to FRiPs in the IgG control" as in the code, you are taking the fragment counts from the bam file of one replicate and "counting" them into the peaks in the control file only. Also, how can I correct this step if I don't have IgG control (that is my case)? I thought about substituting the bed file with my top0.01_stringent.bed of the corresponding replicate, but I'm not sure this is totally correct.
Thank you in advance for your reply.

[yezhengSTAT]

Hello,

Apologize for the confusion. What I mean by "contrast it to FRiPs in the IgG control dataset" is that we can compare the FRiPs in the histone to the FRiPs in the IgG but usually FRiPs in histone are quite high. In that case, we do not need a low baseline, i.e., FRiPs of IgG.

Yes, you can use the top0.01_strigent.bed peak files as an alternative to calculating FRiPs if IgG control is not available.

Thanks,
Ye

[MatteoFiumara]

Dear Ye, thank you very much for your clarification. I will therefore use the sample peak file to calculate the FRiPs. All the best, Matteo.