olechnwin

Thanks! This works.

I feel like my question belong here. Sorry if it isn't. I'm trying to incorporate spike-in normalization for paired-end as OP. I've done step 1-3, skipping step 2 from the...

Hi @taoliu, I have two questions: 1. Can I get the fragment size (`d`) from the output of `callpeak` on the ChIP file? So run the following command, where `${prefix}.bam`...

@taoliu Just want to make sure. The `d` I was referring above is for paired-end reads. So, I can run `macs2 callpeak` to get the `d` for paired-end reads? Thanks!

Thank you so much for your clarification. Appreciate it!

@taoliu , There is something I don't understand. I tried running the subcommands above for the exact same file for treatment and control i.e. `sample1.bam`. At the end, none of...

`@ taoliu, Thank you so much for looking into this. Sorry for the delay. I got distracted... See below for my pipeline. If I understand you correctly, you were suggesting...

@JohnMCMa Thanks for pointing this out. I didn't even notice that `pileup` will ignore the `--extsize` and `-B`. I compared the .bdg out with and without these options and confirmed...

So....I am confused. Which part of the pipeline should be changed?

@taoliu , Now I get it. Thank you so much for taking the time to clarify. Really appreciate it.