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!!
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!
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.