Tao Liu (τν)

The cutoff-analysis for `hmmratac` command is discussed here: https://macs3-project.github.io/MACS/docs/hmmratac.html#choices-of-cutoff-values And a similar cutoff-analysis for `callpeak` command is discussed here: https://macs3-project.github.io/MACS/docs/callpeak.html#cutoff-analysis And if you can generate the cutoff analysis report from...

The fold change values for reasonable peaks are within the lower range. The default parameters for `hmmratac` are `-u 20 -l 10 -c 1.2`. It's possible that we need to...

Also related to #638, it's highly possible that the hidden markov model learned from the low quality data can't capture the expected chromatin structure around accessible sites. This is a...

We are implementing a different emission model for HMM in MACS3 called the Poisson Emission model. During our internal tests, this simple model (compared with the Gaussian Emission model) generated...

@LinearParadox It seems that MACS3 can't read the broadPeak file correctly. Could you share us the top few lines of your broadpeak file?

Your original peak file looks fine to me. It's in the appropriate BED+ format. Only the first six columns are essential and they should be in order: 1. Chromosome; 2....

Hmm... I am wrong with my previous comments. The error was found in: https://github.com/macs3-project/MACS/blob/1d6c38ef4b800a50632d5ddbac79c175bfefe7d4/MACS3/Signal/ReadAlignment.pyx#L307 Here MACS tries to use the MD tag and CIGAR in BAM format to recover the...

This error is caused due to the fact that, the size of a chunk of alignment result in BAM is decoded as larger than 2^32. It shouldn't happen normally since...

Also, thanks for pointing out the error related to: https://github.com/macs3-project/MACS/blob/1d6c38ef4b800a50632d5ddbac79c175bfefe7d4/MACS3/Commands/callvar_cmd.py#L197 Ideally, if there is any error during retrieving reads from a given peak region, MACS3 should skip the peak. And...

I see. This is a very important information. I just tested a bam file from `chromap` and can reproduce your error. Let me check where the problem is.