Chipseq data peak calling issue

Question

[Adyasha]

Hi ,

I'm trying to do analysis of chipseq data. I have 3 samples: Sample1, sample2 and input

I have done QC and then alignment using Bowtie. After that I used samtool to get bam files. Then I have used Picard for duplicate removal. Now I used macs2 for peak calling. I want to see transcription factor binding region.

Then I used

macs2 callpeak -t sample1.bam -c input.bam -f BAM -g genome size --outdir peak calling

But I couldn't get any .bed files from this. I only got .peak, .xlsx, summit.bam.

Then I tried annotating the peaks using this command

.annotatePeaks.pl <.peak(output from macs2)> <hg38>  <output file> 

But this gave me a text file, with some peak ID , starting and end position, but it doesn't give any gene name or ID.

My output doesn't look like this:

Some end columns are missing, and also I think I have very less peaks than expected. Can anyone please help me on this issue?

Thank you