Question: what is the best way to calculate significant differences in tss profiles?
gravatar for Lila M
4 weeks ago by
Lila M 470
Lila M 470 wrote:

Hi everybody, I have different samples that I used to calculate the coverage over specific data set. I did it using deeptools, so my final output is something like this

s1  1,923575916 1,92340092  1,918008392 1,915392666 ...
s2  1,993446863 1,931309701 1,925363124 1,935658019 ...
s3  2,03417052  2,042601134 2,029136552 1,996391637 ...
s4  2,107394697 2,107865284 2,093484711 2,070557165 ...

I would like to test if there are differences on the coverage (by p-value). my first thought was to apply a ks-test, but then I decide to reject it as it test if two samples have the same statistical distribution and not if there are different or not. Does any one else try to address this question before? Thanks!

tss coverage differences • 97 views
ADD COMMENTlink modified 4 weeks ago by ATpoint15k • written 4 weeks ago by Lila M 470

What kind of data is this? How did you produce the counts and what is the experimental setup? Are there replicates?

ADD REPLYlink written 4 weeks ago by ATpoint15k

Hi, there are no replicates, they are ChiP-seq samples in different conditions.

ADD REPLYlink written 4 weeks ago by Lila M 470

For ChIP-seq differential binding use any of the established tools such as csaw or diffbind (or others). These will require replicates. Please use google and the search function to look for posts and opinions on unreplicated data. This question has literally been asked dozens of times before ;-) Do not try to make home-brew statistics, please read the available resources first. E.g. in the csaw manual page 44 what to do without replicates.

ADD REPLYlink written 4 weeks ago by ATpoint15k
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