Comments (2)
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.
Let us know if you find any issues when running hmmratac
in MACS3. We are still optimizing it. @philippadoherty is currently working on reducing the memory usage for this command.
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@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 10 according to the first column. I would guess the settings of '-u 20 -l 10 -c 2' (or -c 5
) should work. We will release a new version soon to address 1) the resolution of cutoff analysis -- to make it with a step of 1 by default #642; 2) to reduce memory usage by a magnitude for large datasets #640 ; 3) to provide a simpler HMM model with Poisson Emission #635. If you can wait, please try the next release.
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Related Issues (20)
- What is the difference between "absolute peak summit" and "summit position" in narrowPeak format? HOT 1
- Q: conversion of output files to UCSC track hub format? HOT 1
- Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS HOT 1
- Feat: Reduction of memory consumption HOT 3
- Q: HMMRATAC output and options for _summit.bed HOT 1
- Feat: Built-in scoring for HMMRATAC HOT 1
- Q: HMMRATAC producing too many peaks HOT 10
- Bug: undefined symbol: __pow_finite HOT 3
- Q: HMMRATAC reproducibility HOT 2
- Bug: Callvar throws an error when run on broadPeak file HOT 15
- Q: impact of sequencing throughput on peak calling HOT 4
- Setting cut-off when using logFE bigWig files from bdgcmp
- Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ? HOT 1
- Bug: OverflowError when running hmmratac
- Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file.
- Feat: Add --call-summits option in MACS3 bdgpeakcall?
- Q: using macs3 to detect peaks on long-read readings
- MACS3 callpeak does not create UCSC Browser ready peak files HOT 1
- Better cutoff levels control for bdgcallpeak cutoff-analysis HOT 1
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