I got the following problem: I use MACS2 (2.1.0.20140616) with the following short commandline:
macs2 callpeak -t file.bam -f bam -g 650000000 -n Test -B --nomodel -q 0.01
It seems to work as I want, but when I convert the .bamfile into .bed via
bedtools bamtobed -i file.bam > file.bed
and use MACS2 on this, I get a lot more peaks. As far as I understand, the .bed-file should contain the same information as the .bam-file, so that's kinda odd.
Any suggestions what's the problem?
Thanks!