Tao Liu (τν)

Hi @decapicone , Windows OS is not supported. I recommend either MacOS or any Linux OS.

@StevenWingett In fact the default values for gsize for hs and mm are determined many years ago on much shorter reads and old assembly. I need to update the numbers...

@StevenWingett Yes. That should be the same numbers from deeptools using the unique-kmers approach. Basically, it should refer to the 'mappable' genome of the reads alignment process.

@huizhen2014 My two comments: 1) When the genome size is small, to keep only 1 unique pair may dilute the real signals. You may consider subsample your ChIP data or...

@huizhen2014 My suggestion is to skip model building and set a fixed value for `extsize`.

@yunfei-dai Your treatment file after downsampling contains 3 million reads, while the input has 4 million reads. I think you can sub-sample them further since the current genome coverage is...

@millerh1 Hi Henry, it seems you didn't set `-g` for `predictd`. By default, it's the human genome size. It means that the `-m MFOLD` is based on the average on...

@MasterChief1O7 Yes. It can be used as a general 'peak caller'. You can get some hints from this article: https://github.com/macs3-project/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands Basically, you can use 'pileup' on BAM file in a...

Hi Xu, thanks for the suggestion. I will consider this feature in the next release.

@yirenheihei Could you share me the command line and the runtime message?