Hello,

I created bigwig file from a treat_pileup.bdg file generated by macs2 and also used treat_pileup.bdg and control_lambda.bdg with macs2 bdgcmp.

Here is my codes;

peak calling

macs2 callpeak -t sample.bam -c sample_input.bam -g hs -f BAM -q 0.001 --bdg --outdir /folder -n sample

bedGraphToBigWig sample_treat_pileup.bdg hg19.len sample_treat_pileup.bw

fold enrichment tracks

macs2 bdgcmp -t sample_treat_pileup.bdg -c sample_control_lambda.bdg -o sample_foldEnrichment.bdg -m FE

sort -k 1,1 -k2,2n sample_foldEnrichment.bdg > sample_foldEnrichment_sorted.bdg

bedGraphToBigWig sample_foldEnrichment_sorted.bdg hg19.len sample_foldEnrichment_sorted.bw

When I see the tracks on IGV,

{UP: macs2 treat_pileup BOTTOM: Fold enrichment} the tracks look very different. Peak locations which are to focus, are different, right? Also highest peaks are changing between two signals.. I read that fold enrichment (using the control_lambda) dedcut the noise. So, Can I assume that the true signal can be seen in fold enrichment tracks?

Thank you.