Chipseq data peak calling issue

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 these files .

Then I tried annotating the peaks using this command <.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 .

enter image description here

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

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