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.
