MACS
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macs3-project
MACS -- Model-based Analysis of ChIP-Seq
**Describe the bug** Python 3.10 has a change, I think in cython where use_tracing is now replaced by tracing. It causes failure to install at Prob.c, MACS2/IO/Parser.c and probably more....
Hi, I have access to bigWig file from an ATACseq experiment, but I do not have the original fastqs nor the bam files of the alignment. I wanted to know...
**Describe the bug** The code checks to see if the Python version is less than 3.6. It does this by using the floating point equivalent of the version number. This...
Hi tao, I am using macs call peak, when i set q cutoff with 1 and 0.05, the results show a little different, set "-q 1", with ~1500 peaks with...
### Discussed in https://github.com/macs3-project/MACS/discussions/522 Originally posted by **luised94** September 19, 2022 Wasnt sure if it should be on issue or discussion board. Hello, I have been trying to use MACS3...
**Describe the solution you'd like** I'd like the option to calculate scores for peaks when running MACS3 HMMRATAC, similar to the original HMMRATAC implementation (the old command line option `--score...
Hello, I am using macs3 hmmratac mode for ATAC-Seq samples without control samples. I am getting 0 value for columns 13 through 15 in accessible peaks output. Is this related...
Hi, I have the same question as in (https://github.com/macs3-project/MACS/issues/592#issue-1867137129) 1. and in general, are the columns generated here the same as in the original paper? (https://github.com/LiuLabUB/HMMRATAC/blob/master/HMMRATAC_Guide.md#commandline-options), 2. Another question: In...
**Use case** I run macs2 with below command per q-value cut-off 0.05, 0.1 and 0.5 `macs2 callpeak -f BAMPE -g hs -n sample_ID -t sample_remove_duplicate_mito.bam --outdir ./peak --min-length 100 --q...
Hello, I'm working with a single cell ATAC dataset in an organism with a very large genome (32 Gbp). Therefore, the number of reads is quite high ~300M and I...
