Welcome to MPRAflow’s documentation!¶
This pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRA) to create count tables for candidate sequences tested in the experiment.
- Installation & Getting Started
- Instructions for the Installation of the program and some examples to get you started.
- MPRAflow Workflows
- An overview of how MPRAflow works and documentation for the MPRAflow sub workflows.
- MPRAflow Examples
- Muliple examples from the literature are listed for every sub workflow in MPRAflow.
- Project Information
- More information on the project, including the changelog, list of contributing authors, and contribution instructions.
Quick Example¶
nextflow run count.nf --dir "fastQFolder" --experiment-file "experiment.csv" --design "design.fa" --association "bc_map.pickle" --m 1 -resume --mpranalyze --outdir "output"
Features¶
Association: | This utility takes in library association sequencing data (FASTQ) and a design file (FASTA) to assign barcodes to the corresponding elements tested. Functionality includes filtering for quality and coverage of barcodes. This utility must be run before the COUNT utility. |
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Count: | This utility processes sequence data (FASTQ) of barcodes from the DNA and RNA fractions of the MPRA experiment and outputs count tables labeled with the element tested and a label provided in the design file. This utility can process multiple replicates and conditions in a parallelized manner. Based on a user specified flag, the pipeline will either output normalized activity for each tested sequence, or will combine the results into a single count matrix compatible with MPRAnalyze. |
Saturation mutagenesis: | |
This workflow is about getting single variant effect from a target with multiple mutations generated by error-prone PCR. The workflow takes counts (e.g. from the count workflow), combines them with an association file (variants to barcodes) and uses a generalized linear model to to detect single variant effects. |
Feedback¶
The best place to leave feedback, ask questions, and report bugs is the MPRAflow Issue Tracker.