Which data should I select in Encode chip-seq data?

Question

[tinyimp80]

I want to analyze the ENCODE ChIP-seq data. In this case, which data should I select?

I will analyze the peaks from replicate 1 and 2 and detect the common peaks.

Should I download the files 'ENCFF162ADN' (replicate 1) and 'ENCFF881CNC' (replicate 2)?

Alternatively, should I download all the isogenic replicates 1 and 2, and then merge each pair of isogenic replicates separately?

In this picture, it seems to indicate the latter.

What should I do? Please help me!!

Thanks

Answer 1

[ATpoint]

What you have there is an input control, so there is not going to be any meaningful peaks. In general, you would need the replicates, but actually ENCODE provides the IDR peak files already, that is peaks reproducible between the replicates assessed by Irreproducible Discovery Rate, so why not using that?

[tinyimp80]

Actually, I know those are input control.

I do have a chip-seq for peak calling. I was wondering which one I should choose if it looks like the one in the picture above.

The data shown in the photo above is an example.

The reason I don't use IDR is that I'm studying and practicing before analyzing with a my chip-seq data.

Thank you for your comment!

[tinyimp80]

My English is not very good, so my explanation is a bit lacking.

I'm asking because I don't know which fastq file to use to create a SAM(BAM) file to use for input.

I don't know if I need to download all the fastq files for isogenic replicate 1 to create one SAM file, or if I can just use one fastq file from isogenic replicate 1 to create the SAM file.