This repository is for systemic MPRA code.
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
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)
Andreas Pfenning ([email protected])
Irene Kaplow ([email protected])
Ashley Brown ([email protected])
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).