``` Some help needed regarding Chip-seq analysis. I use MACS3 to call the peaks. Earlier, I had used a Chip-seq sample data from the internet and obtained around 60,000 peaks/sorted.bam file from the pipeline that I use.

But now I am getting around 50 peaks only in the sample which we prepared. The input IP control is also there. How do we know whether there is a problem in the sample or the software/pipeline/MACS3 ?

This standalone tool is not part of Bioconductor, you would be better off asking at biostars.org or bioinformatics reddit. Generally, two things: a) Look at the data in the IGB browser to "see" data, check if there is separation of peaks from noise. IP simply could have failed, and b) you have super low depth. Just about 1.7mio reads for the IP, maybe library is stronghly undersequenced.