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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!

Timur Shtatland
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N. F.
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  • You probably want to tag the appropriate languages and frameworks. It will be hard for people to help you otherwise. – Zachary Dow Nov 10 '15 at 22:16

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