title: Different results with MACS2 when Peakcalling with .bed or .bam
body: <p>I got the following problem: 
  I use MACS2 (2.1.0.20140616) with the following short commandline:</p>
  
  <pre><code>macs2 callpeak -t file.bam -f bam -g 650000000 -n Test -B --nomodel -q 0.01
  </code></pre>
  
  <p>It seems to work as I want, but when I convert the .bamfile into .bed via </p>
  
  <pre><code>bedtools bamtobed -i file.bam &gt; file.bed
  </code></pre>
  
  <p>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. </p>
  
  <p>Any suggestions what's the problem?</p>
  
  <p>Thanks!</p>