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MAJIQ.smk

Snakemake workflow for differential RNA splicing analysis using MAJIQ.

Note

Please make sure that you have Singularity and Snakemake installed on your system and cloned the SnakeNgs repository.

Workflow

MAJIQ.smk rulegraph

The rulegraph was created by snakevision.

  1. Parse the experiment table to create a setting file for MAJIQ.
  2. Build splicegraph using MAJIQ build.
  3. Differential splicing analysis using MAJIQ heterogen and deltapsi.
  4. Make a tab-separated summary of the results using MAJIQ voila tsv.
  5. Modulize the results using MAJIQ voila modulize.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/MAJIQ.smk \
--configfile /path/to/config.yaml \
--cores <int> \
--use-singularity \
--rerun-incomplete

config.yaml should contain the following information:

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workdir: /path/to/output
container: /path/to/singularity_image
experiment_table: /path/to/experiment_table.tsv
gff: /path/to/reference_transcriptome.gff3
genome: hg19 # hg19, hg38, mm10, mm39, etc.
strandness: None # [None, forward, reverse]
  • /path/to/output is the directory where the output files will be saved.
  • /path/to/singularity_image is the path to the Singularity image file for MAJIQ.

Note

As of now, there is no public Docker/Singularity image available for MAJIQ. You need to build the image by yourself. Please refer to the MAJIQ installation guide for more information.

  • /path/to/experiment_table.tsv is a tab-separated file, which is same as the one used in Shiba.
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sample  bam group
sample1 /path/to/sample1.bam    Ref
sample2 /path/to/sample2.bam    Ref
sample3 /path/to/sample3.bam    Ref
sample4 /path/to/sample4.bam    Alt
sample5 /path/to/sample5.bam    Alt
sample6 /path/to/sample6.bam    Alt

The group column must be specified as Ref or Alt. This workflow will perform the differential splicing analysis between the two groups.

  • /path/to/reference_transcriptome.gff3 is the reference transcriptome in GFF3 format (e.g. Homo_sapiens.GRCh38.106.gff3 for human transcriptome).
  • genome is the genome version used in the analysis (e.g. hg19, hg38, mm10, mm39, etc.).
  • strandness is the strandness of the RNA-seq data. (None, forward, reverse)

Docker image used in the workflow

No public Docker image is available for MAJIQ.