MAJIQ


Majiq Parameters

In the previous quick start section we described a general execution pipeline for MAJIQ, but those three commands have many other parameters that can be adjusted to modify MAJIQ's behavior.

Builder

majiq build [-h] transcripts -c CONF --output OUTDIR [-j NTHREADS] [--silent] [--debug] [--min-experiments MIN_EXP] [--k K_samples] [--m M_samples][--min-denovo MIN_DENOVO] [--minreads MINREADS] [--min-intronic_cov MIN_INTRONIC_COV] [--minpos MINPOS] [--disable-denovo] [--disable-ir] [--markstacks PVALUE_LIMIT]

Mandatory arguments:

  • transcripts: Transcriptome file with the annotation database. Currently, we accept GFF3 format. For a better description, see the annotation file section. transcripts can be a majiq DB file generated with DB.npz name from a previous majiq build execution.
  • -c/--conf CONFIG_FILE: This is the configuration file for the study. This file should define the files and the paths for the bam files, the read length, the genome version, and some other information needed for the Builder. For a more detailed information, please check the configuration file section.
  • -o/--output OUTDIR: Directory where the output will be placed. MAJIQ Builder has a set of output files .majiq per each bam file and one splicegraph.sql. These files will be the input files in the next steps of the analysis.

Optional arguments:

  • -h, --help: Show help message and exit
  • -j/--nproc NTHREADS: Number of threads to use.
  • --prebam: prebam option will assume that the bam analysis was done before in the specified output folder. Causes the Builder to skip redoing this step and look for the temporary files that should be already generated.

  • --disable-denovo: Avoid de novo detection of junction, splice-sites, and exons. This will speedup the execution but reduce the number of LSVs detected.

  • --disable-ir: Avoid intron retention detection. This will speedup the execution but reduce
  • the number of LSVs detected.
  • --k K: Number of positions to sample per iteration. [Default: 50]
  • --m M: Number of bootstrapping samples. [Default: 100]
  • --minreads MINREADS: Minimum number of reads threshold combining all positions in a LSV to consider that the LSV "exists in the data". [Default: 3]
  • --minpos MINPOS: Minimum number of start positions with at least 1 read in a LSV to consider that the LSV "exists in the data" [Default: 2]
  • --min-intronic_cov MIN_INTRONIC_COV: Minimum number of reads on average in intronic sites, only for intron retention. [Default: 1.5]
  • --min-experiments MIN_EXP: Used to lower the threshold for group filters. min_experiments is the minimum number of experiments where the different filter checks in order to pass an lsv or junction.
  • --min-denovo MIN_DENOVO: Minimum number of reads threshold combining all positions in a LSV to consider that denovo junction is real". [Default: 2]
  • --markstacks MARKSTACKS: Mark stack positions. Expects a p-value. Use a negative value in order to disable it. [Default: 1e-07]

Logger arguments:

  • --logger LOGGER_PATH: Path for the logger. Default is output directory
  • --silent : Boolean argument used to silence the logger.
  • --debug: Activate this flag to activate debug messages.

PSI

majiq psi [-h] [-j NTHREADS] -o OUTDIR -n NAME [--logger LOGGER] [--silent] [--debug] [--min-experiments MIN_EXP] [--minreads MINREADS] [--minpos MINPOS] <!-- [--weights WEIGHTS] [--weights-alpha WEIGHTS_ALPHA] [--weights-threshold WEIGHTS_THRESHOLD] [--weights-local LOCAL] --> files [files ...]

Mandatory arguments:

  • files: .majiq file[s] that were created by the MAJIQ Builder execution
  • -n/--name NAME: The name that identifies the quantification group.
  • -o/--output OUTDIR: PSI output directory. It will contain the psi.voila file once the execution is finished. - Optional arguments:
  • -h, --help: Show help message and exit
  • -j/--nprocs NTHREADS: Number of threads to use.
  • --minreads MINREADS: Minimum number of reads to pass the quantifiable threshold combining all positions in a LSV to considered. [Default: 10]
  • --minpos MINPOS: Minimum number of start positions with at least 1 read in a LSV to considered. [Default: 3]
  • --min-experiments MIN_EXP: Use to alter the threshold for group filters. min_experiments is the minimum number of experiments where the different filter checks must be met in order to consider LSV or junction quantifiable.

Logger arguments:

  • --logger LOGGER_PATH: Path for the logger. Default is output directory
  • --silent : Boolean argument used to silence the logger.
  • --debug: Activate this flag to activate debug messages.

DeltaPSI

majiq deltapsi -grp1 FILES1 [FILES1 ...] -grp2 FILES2 [FILES2 ...] -n NAMES [NAMES ...] -o OUTDIR [-h] [-j NTHREADS] [--logger LOGGER] [--silent] [--debug] [--min-experiments MIN_EXP] [--minpos MINPOS] [--minreads MINREADS] [--binsize BINSIZE] [--default-prior] [--prior-minreads PRIORMINREADS] [--prior-minnonzero PRIORMINNONZERO] [--prior-iter ITER]

Mandatory arguments:

  • -grp1 FILES1 [FILES1 ...]: Set of .majiq file[s] for the first condition
  • -grp2 FILES2 [FILES2 ...]: Set of .majiq file[s] for the second condition
  • -n/--names NAMES [NAMES ...]: _cond_id1_ _cond_id2_: group identifiers for grp1 and grp2 respectively.
  • -o/--output OUTDIR: PSI output directory. It will contain the deltapsi.voila file once the execution is finished.

Optional arguments:

  • -h, --help: Show help message and exit
  • -j/--nprocs NTHREADS: Number of threads to use [Default: 4].
  • --minreads MINREADS: Minimum number of reads to pass the quantifiable threshold combining all positions in a LSV to considered. [Default: 10]
  • --minpos MINPOS: Minimum number of start positions with at least 1 read in a LSV to considered. [Default: 3]
  • --min-experiments MIN_EXP: Use to alter the threshold for group filters. min_experiments is the minimum number of experiments where the different filter checks must be met in order to consider LSV or junction quantifiable.
  • --binsize BINSIZE: The bins for PSI values. With a BINSIZE of 0.025 (default), we have 40 bins
  • --default-prior: Use a default prior instead of computing it using the empirical data
  • --prior-minreads PRIORMINREADS: Minimum number of reads combining all positions in a junction to be considered (for the 'best set' calculation). [Default: 20]
  • --prior-minnonzero PRIORMINNONZERO: Minimum number of positions for the best set.
  • --prior-iter ITER: Max number of iterations of the EM

Logger arguments:

  • --logger LOGGER_PATH: Path for the logger. Default is output directory
  • --silent : Boolean argument used to silence the logger.
  • --debug: Activate this flag to activate debug messages.