Command line to use HMMRATAC in MACS3

[tahirsajid]

Hi,
I went through documentation of MACS3. I could not find the command line to use HMMRATAC in MACS3. Can somebody please share the command line?

[mrendleman]

It looks like a lot of the documentation for macs3 version 3.0.0b1 is incomplete, but the -h help message for hmmratac is informative:

$ macs3 hmmratac -h
usage: macs3 hmmratac [-h] -b BAM_FILE [BAM_FILE ...] [--outdir OUTDIR] [-n NAME] [--save-digested] [--save-states]
                      [--save-likelihoods] [--save-training-data] [--no-fragem] [--means EM_MEANS EM_MEANS EM_MEANS EM_MEANS]
                      [--stddevs EM_STDDEVS EM_STDDEVS EM_STDDEVS EM_STDDEVS] [--binsize HMM_BINSIZE] [-u HMM_UPPER] [-l HMM_LOWER]
                      [--maxTrain HMM_MAXTRAIN] [--training-flanking HMM_TRAINING_FLANKING] [--model HMM_FILE] [-c PRESCAN_CUTOFF]
                      [--minlen OPENREGION_MINLEN] [--randomSeed HMM_RANDOMSEED] [--decoding-steps DECODING_STEPS] [-e BLACKLIST]
                      [--keep-duplicates] [--verbose VERBOSE] [--buffer-size BUFFER_SIZE]

optional arguments:
  -h, --help            show this help message and exit

Input files arguments:
  -b BAM_FILE [BAM_FILE ...], --bam BAM_FILE [BAM_FILE ...]
                        Sorted BAM files containing the ATAC-seq reads. If multiple files are given as '-t A B C', then they will
                        all be read and pooled together. REQUIRED.

Output arguments:
  --outdir OUTDIR       If specified all output files will be written to that directory. Default: the current working directory
  -n NAME, --name NAME  Name for this experiment, which will be used as a prefix to generate output file names. DEFAULT: "NA"
  --save-digested       Save the digested ATAC signals of short-, mono-, di-, and tri- signals in three BedGraph files with the
                        names NAME_short.bdg, NAME_mono.bdg, NAME_di.bdg, and NAME_tri.bdg. DEFAULT: False
  --save-states         Save all open and nucleosomal state annotations into a BED file with the name NAME_states.bed. DEFAULT:
                        False
  --save-likelihoods    Save the likelihoods to each state annotation in three BedGraph files, named with NAME_open.bdg for open
                        states, NAME_nuc.bdg for nucleosomal states, and NAME_bg.bdg for the background states. DEFAULT: False
  --save-training-data  Save the training regions and training data into NAME_training_regions.bed and NAME_training_data.txt.
                        Default: False

EM algorithm arguments:
  --no-fragem           Do not perform EM training on the fragment distribution. If set, EM_MEANS and EM.STDDEVS will be used
                        instead. Default: False
  --means EM_MEANS EM_MEANS EM_MEANS EM_MEANS
                        Comma separated list of initial mean values for the fragment distribution for short fragments, mono-, di-,
                        and tri-nucleosomal fragments. Default: 50 200 400 600
  --stddevs EM_STDDEVS EM_STDDEVS EM_STDDEVS EM_STDDEVS
                        Comma separated list of initial standard deviation values for fragment distribution for short fragments,
                        mono-, di-, and tri-nucleosomal fragments. Default: 20 20 20 20

Hidden Markov Model arguments:
  --binsize HMM_BINSIZE
                        Size of the bins to split the pileup signals for training and decoding with Hidden Markov Model. Must >= 1.
                        Smaller the binsize, higher the resolution of the results, slower the process. Default = 10
  -u HMM_UPPER, --upper HMM_UPPER
                        Upper limit on fold change range for choosing training sites. Default: 20
  -l HMM_LOWER, --lower HMM_LOWER
                        Lower limit on fold change range for choosing training sites. Default: 10
  --maxTrain HMM_MAXTRAIN
                        Maximum number of training regions to use. Default: 1000
  --training-flanking HMM_TRAINING_FLANKING
                        Training regions will be expanded to both side with this number of basepairs. The purpose is to include
                        more background regions. Default: 1000
  --model HMM_FILE      A JSON file generated from previous HMMRATAC run to use instead of creating new one. When provided, HMM
                        training will be skipped. Default: NA

Peak calling arguments:
  -c PRESCAN_CUTOFF, --prescan-cutoff PRESCAN_CUTOFF
                        The fold change cutoff for prescanning candidate regions in the whole dataset. Then we will use HMM to
                        predict states on these candidate regions. Higher the prescan cutoff, fewer regions will be considered.
                        Must > 1. Default: 1.2
  --minlen OPENREGION_MINLEN
                        Minimum length of open region to call accessible regions. Must be larger than 0. If it is set as 0, it
                        means no filtering on the length of the open regions called. Please note that, when bin size is small,
                        setting a too small OPENREGION_MINLEN will bring a lot of false positives. Default: 100

Misc arguments:
  --randomSeed HMM_RANDOMSEED
                        Seed to set for random sampling of training regions. Default: 10151
  --decoding-steps DECODING_STEPS
                        Number of candidate regions to be decoded at a time. The HMM model will be applied with Viterbi to find the
                        optimal state path in each region. bigger the number, 'possibly' faster the decoding process, 'definitely'
                        larger the memory usage. Default: 1000.
  -e BLACKLIST, --blacklist BLACKLIST
                        Filename of blacklisted regions to exclude (previously was BED_file). Examples are those from ENCODE.
                        Default: NA
  --keep-duplicates     Keep duplicate reads from analysis. By default, duplicate reads will be removed. Default: False
  --verbose VERBOSE     Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2:
                        show process information, 3: show debug messages. DEFAULT:2
  --buffer-size BUFFER_SIZE
                        Buffer size for incrementally increasing internal array size to store reads alignment information. In most
                        cases, you don't have to change this parameter. However, if there are large number of
                        chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order
                        to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested
                        for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000

TBA...

Hope this helps!

[tahirsajid]

Yeah looks like that. Thank you.

[kbarrr]

macs3 hmmratac -i M1_dedup_noM_sorted.bam -f BAMPE

i tried this