MPRAscore

Robust and non-parametric analysis of massively parallel reporter assays (MPRA)

MPRAscore infers allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence.

Running MPRAscore

MPRAscore is implemented in C++. It can be compiled from the source code. Precompiled executables for Windows, Linux, and Mac are included in binaries/.

For help:

mprascore -?

Example:

Example files are included in Example/. To run MPRAscore on example data:

mprascore L363_barcode_map.txt L363_barcode_counts.txt -RNAcols:L363_RNA_1,L363_RNA_2,L363_RNA_3 -DNAcols:L363_DNA_1,L363_DNA_2,L363_DNA_3 L363_results.txt -p:1000

Data: Raw fastq files for the example data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA554195.

Citation:

Niroula A, Ajore R, Nilsson B. (2019) MPRAscore: robust and non-parametric analysis of massively parallel reporter assays. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz591

Contact:

For any queries, contact [email protected]