Difference b/w version 2.1.0.20150731 and version 2.1.1.20160309

[Aarthi Mohan]

Hi,

I recently updated MACS2 using 'pip', and re-run the peak calling. I found that the broad peak call numbers have increased so much. How is this?

I have used the same parameters in both the run, but still get different peak numbers. There is also a change in the number of narrow peaks, but not this dramatic.  I use BAMPE, since  my data is paired-end. 

# broad peaks b/w the two version:

              v2.1.0  v2.1.1

Sample1 914   2250

Sampe2  5   3860

What is the difference in the broad peak calling between the two versions?

Appreciate your help!

Thanks,

Aarthi

[Moshe Olshansky]

Hi Aarthi,

How did you get your data into BEDPE format?
Please keep in mind that BEDPE format used by MACS2 is NO the "standard" BEDPE format like in bedTools (which has 9 fields).

Best regards,
Moshe.

[Aarthi Mohan]

Hi Moshe,

I am using BAMPE, and still see a huge difference in broad peak call numbers between the versions.

I have used BEDPE too once. I used bedtools to convert BAM to BED, and use columns 1,2, and 6 from it to create the expected BEDPE file.

Thanks,
Aarthi