Create the "control_sample.txt "

michelleapaz / T3E

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Create the "control_sample.txt " #4

Closed ngualand closed 8 months ago

ngualand commented 9 months ago

Hi,

I need to compare the binding sites of 2 ChIP seq experiments and I have 2 samples (control and treated) and their corresponding input files. How can I prepare my "control_sample.txt " file. Should I put in the first line the input files and in the second one the ChIPeed samples? Supose the control file is called A and the treated samples is called B with their respective inputs A_I and B_I, is the following file correct?

A_I B_I A B

Thank you very much for the help

michelleapaz commented 9 months ago

Hello,

Thanks for your message.

As I understand your message, the "control_sample.txt" file should be:

A_I A B_I B

Kind regards,

Michelle

ngualand commented 9 months ago

Hi Michelle,

Thank you very much for the reply. Now I understand.

I have ti additional questions.

Can I compare the enrichment between 2 samples? For example KO vs WT samples?
I m now running the software on about 70 GB bam files (that also contain multimapping reads) do you expect the software working on that files dimension?

Many Thanks.

michelleapaz commented 8 months ago

Hi,

Using T3E you will obtain as output the enrichment (log2FC) and an associated p-value for each TE family/subfamily ("group") for the KO (A) and WT (B) samples. The comparison between A and B can be seen as how much enrichment of a specific TE group in B is greater compared to A. You can, of course, design your experiment to include replicates as well.
T3E is able to run files of such sizes, however it depends on the available RAM. It is possible (and suggested in such cases) to down-sample (default is 20 million reads), but you can also use a different number of iterations (default is 100).

What I would suggest you is to run only one iteration and adjust those parameters according to your need.

Best!

Michelle

ngualand commented 8 months ago

Many Thanks,

Nicolò

ngualand commented 8 months ago

Thank you very much for the help,

I have run he software as suggested and everything works smoothly. For some TEs families I have obtained a p.value = 0 (iterations = 100). Should I consider this as highly significant (i.e The p.value is too low to be computable) or Should I consider this an error/warning ?

Thanks,

Nicol0'

michelleapaz commented 8 months ago

Hi Nicolo,

I am glad T3E worked smoothly.

You should consider these cases statistically significant (p-value < 0.01), when using 100 iterations.

Regards,

Michelle