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
.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.
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