How to find time point of read counts?

Q&A
1

I wonder can I find a readcounts file like this? In terms of experiments, in studying each cell line, what is the study design, how many time points siRNAs were measured, how many replicates per time point?

image001
image001791×199 74.7 KB

2

Hi cyang,

We do not offer files in that format. You can download the matrix of readcounts instead. To understand the details of the experimental design, please read the documentation. It will point you to some references for further reading as well.

3

Thanks! I wander can you tell me what “p5,p6” in colname of readcounts matrix means? Is it means passage?

image001.png920×84 11.7 KB

Best,

Chen

4

Yup, that’s correct.

5

Hi,

I want to use MAGeCK to calculate the depmap data, but I noticed that the input readcounts matrix of MAGeCK needs initial and final data, I want to know how should I look for this part of information in the depmap? The data provided by depmap seems to only have 21 days of final data.

Best,

Chen

6

Hi Chen,

The correct early reference is the pDNA. The README and associated references explain how to identify which columns are pDNA and how we combine them.

7

Hi,

Thanks for your reply! I wonder if their initial reads are the same for different cell lines of the same batch (say pDNA2)?

Best,

Chen