Tao Liu (τν)

BEDPE support has been added #580 CRAM support will be added in the future. I need some planning on how to implement that. We didn't use any third-party libs to...

@mcsimenc the 5th column, according to definition of [narrowPeak](https://genome.ucsc.edu/FAQ/FAQformat.html#format12) represent the peak score. In MACS, the score is the integar form of 10 x -log10(qvalue) (9th column). In the callpeak.md...

@StevenKrzysztof It seems that there is an abnormally large 'fragment length' in the data can't be assigned to either short fragment, mono-nucleosome, di-nucleosome, or tri-nucleosome. I think the best way...

@cbravo93 Please install MACS3, which has this problem solved. https://pypi.org/project/MACS3/

Hello @kbarrr the tutorial on using `hmmratac` command in the MACS3 (version 3.0) can be found here: https://macs3-project.github.io/MACS/docs/hmmratac.html The command line options are different from the `callpeak` command in MACS3....

@kbarrr Thanks for the information! However, the resolution of the cutoff analysis report is not good enough for me to judge where the cutoff should be -- each step is...

It is possible that certain functions that we used from Numpy/Scipy/sci-kit-learn/hmmlearn escaped the randomSeed setting. But we do have github action testing for macs3 code to make sure that everytime...

@jowodo What's the version of Cython?

Thanks for your report! We will switch back to `-O3` in future releases, to avoid the `-ffast-math` optimization.

One thing you can try is to increase the cutoff for calling candidate regions in the macs3 version of `hmmratac` using the option for prescan-cutoff `-c`. And perhaps first run...