Tao Liu (τν)

Hi @zhangpicb really strange, since I normally assume the opposite. Could you also load the 'bedGraph' files from MACS in IGV as well?

Hi @yue131 , I would recommend using the paired-end mode through `-f BAMPE` if you are focusing on the accessible region between the Tn5 insertion sites of a read pair....

You also found the discussion in #195, where @kwcurrin had a good point that in certain circumstances, where you have a dominant abundance of the nucleosomal fragments in the ATAC-seq...

@wangc1106 1. Your ATAC-seq is paired-end data, so, when you converted it to BED with bedtools, the pairing information, along with all bitwise flags, is lost. Therefore you will get...

@tudumanne Thanks for asking the question! When I wrote the step-by-step tutorial to call peaks using subcommands in 2017, MACS2 can't do `pileup` subcommand on paired-end data. From v2.1.2, MACS2...

@tudumanne You are welcome!

@olechnwin 1. Yes. You can get the `d` by running `macs2 callpeak`. Or follow the step 1 and step 2 of the advanced tutorial. 2. Right.

Yes. `macs2 callpeak` will give you the average insertion length of unique pairs in your PE library.

@olechnwin Could you provide the entire pipeline on how you ran the subcommands? But based on your reply (https://github.com/taoliu/MACS/issues/356#issuecomment-603890497) I noticed that there are some differences between your subcommands and...

@JohnMCMa Thanks for your input! You are totally right :) In our regular `callpeak` command, if PE data is used, signals for the treatment/ChIP track will be computed by piling...