sysMPRA

This repository is for systemic MPRA code.

Scripts

designMPRA1Sequences.sh: code for designing sequences related to MEF2C binding for the gMPRA

getEnsemblCoordinatesFromGff3.py: code for obtaining gene coordinates from gff3 files

convertFIMOToMotifHitBed.py: code for converting motif hits from FIMO from the MEME suite to a bed file

chooseBestScramble.py: code for choosing the shuffled sequence with the least significant motif match

filterFastaFile.py: filter a fasta file based on the fasta headers

predictMPRASequences.sh: make open chromatin predictions for gMPRA sequences

arrayProc: directory with scripts for processing MPRA data

Dependencies

bedtools version 2.26.0

meme suite version 4.12.0

liftOver (UCSC Genome Browser utility)

python version 2.7.17 (chooseBestScramble.py also works with python version 3.7.6)

numpy version 1.13.3

biopython version 1.70

twoBitToFa (UCSC Genome Browser utility)

OCROrthologPrediction (https://github.com/pfenninglab/OCROrthologPrediction)

Contacts

Andreas Pfenning (apfenning@cmu.edu)

Irene Kaplow (ikaplow@cs.cmu.edu)

Ashley Brown (arb1@andrew.cmu.edu)

Reference

Brown AR, Fox GA, Kaplow IM, Lawler AJ, Phan BN, Ramamurthy E, May GE, Wirthlin ME, Chen Z, Su Q, McManus CJ, Pfenning AR. An in vivo massively parallel platform for deciphering tissue-specific regulatory function. biorXiv. https://www.biorxiv.org/content/10.1101/2022.11.23.517755v1 (2022).