apply cicero in bulk of ATAC-seq

[deb...@icloud.com]

Since cicero is used in scATAC-seq, is there any idea to apply cicero on a bulk of ATAC-seq?

I got more than 10 set of bulk ATAC-seq data,

Could I just simply aggregate those data sets to generate a cicero input matrix?

[Hannah Pliner]

Hello,

Cicero was only intended to be used for single-cell ATAC, and we have no experience running it on bulk. I suspect that 10 samples will not be sufficient (nor be sufficiently homogenous) to generate good results. If you do try it, I would be certain that you validate your connections with some orthogonal dataset.

Best,

Hannah

[deb...@cgmh.org.tw]

Dear Hannah,

thanks for the reply,

I will go on trying to use cicero on bulk data.

Now I got 10 narrowpeak bed file. I tend to merge those peak files into an aggregated peak file, and count fragments separately to generate the count matrix.

Is there any suggusted toolkit to generate this aggregated peak file? I might try bedtool intersect first.

thanks

Debbie  

Hannah Pliner於 2020年2月24日星期一 UTC+8下午9時06分31秒寫道：

[Hannah Pliner]

Hi Debbie, 

Sorry for the delay - I have used bedtools in the past for similar problems, so I think you're on the right track.

Best,

Hannah

[mzwa...@gmail.com]

Hi Debbie,

I am planning to follow the same route and aggregate about 32 bulk-ATAC seq samples. How do you go about aggregating the files? Do you script them out in R, if so would you please be willing to share with me your code -- or do you aggregate them using a different tool? 

I am green hand at bioinformatics :) 

Thanks,

Mzwanele