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I have a ChipSeq .fastq file that was created in 2014, along with a control. V7.1 was the latest at that time. I successfully align it to the latest version of x.laevis (using bowtie2), sort it/index it and run mac2 callpeaks on it. The problem is I'm only getting 10 peaks which isn't right. My callpeaks line is:
macs2 callpeak -t E2F4.aligned.bam -c E2F4_control.aligned.bam -f BAM -n E2F4_xl --outdir ../peaks
Are there options that I'm missing that's limiting my output? I tried to google this and couldn't find anything. Before I give up on this I thought I would ask this community to see if there's anything else I can do to get better data.
Thanks in advance
Before you post anywhere else, do the due diligence and inspect data on the IGV. Make a bigwig file from the sorted bam (for example deeptools bamCoverage with binsize 1) and see whether visually there are peaks. Can well be that the ChIP/antibody is just crap and 10 peaks is just what it is => a lot of noise in a poor dataset. In case you come to the conclusison that peaks are there and should be called, feel free to post at biostars.org with screenshots and code plus details that kight hep debugging the peak calling.
I will...thank you both