Hi guys, I have a question about MACS2 to call peaks from either chip-sew or ATAC seq. When I used macs2 to call peaks, the program used hs for human genome, which corresponds to hg18. But in later analysis, when I useD homer to find motifs in peaks, I used hg19. Is there any influence since the position of genes in different genome project is different? Thanks. Here is the scripts: /usr/local/macs2/latest/bin/macs2 callpeak --outdir -t * -c * -n * -g hs -B --keep-dup 1 --nomodel --shift -75 --extsize 150 -q 0.01 /home/users/homer/bin/findMotifsGenome.pl *.txt hg19 *_discover/ -size -100,100 -mask -S 50
The difference is minimal at best, at least in the peak calling. I remember reading a post by Istvan once that said that as long as the first number of the effective genome size is the same (ex. 2.7 billion in hg18, 2.8 billion in hg19) then you should be fine.