Paired end and single end with MACS2
2
3
Entering edit mode
5.4 years ago

Dear all,

this is my fist ChIP Seq analysis ever so I need some guidance from the more experienced ones. I am now at the step of peak calling and decided to use MACS2 for this. My question is: if my control is SE but my treated samples are PE how should I handle this? Is this a problem? I think, that using only one strand for the PE is not a good idea.

Any suggestions?

Thanks a lot! F

ChIP-Seq MACS2 peak calling • 5.9k views
ADD COMMENT
3
Entering edit mode
5.4 years ago
Ian 5.8k

You should be able to run both files using --format BAM, MACS2 should just use the 5' read of each pair in the PE file. As a SE analysis the fragment length will be calculated by cross correlation, however if you run MACS2 with the PE ChIP on its own then you can get the value 'd' from the log info. Then, when you run the SE analysis with the control you can use --nomodel --extsize 'd' (as its integer value'.

ADD COMMENT
1
Entering edit mode

Thank you for the detailed answer! :)

ADD REPLY
2
Entering edit mode
5.4 years ago

Your description hints at a large underlying batch-effect in your data.

Anyway, the least biased route would be to just use read #1 from your treatment samples (possibly trimming things down a bit if the read lengths were vastly different).

ADD COMMENT
0
Entering edit mode

Thank you for your comment!

ADD REPLY

Login before adding your answer.

Traffic: 1880 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6