This is modified version of CODA for RtcB ligation based deep mutational scanning. It is used to generate the base-pairing map from deep mutational sequencing data of RNA ribozyme, with the method introduced in the paper. We also provided the processed .ra files (L1-fl.ra, L1-mini.ra, OR-fl.ra) from different DMS experiments.
Before running this pipline, make sure these programs were correctly installed.
PEAR (https://cme.h-its.org/exelixis/web/software/pear/)
python 2.7.15
samtools 0.0.18
java 1.7.0_85
bash run.sh $DNAFILE1 $DNAFILE2 $RNAFILE1 $RNAFILE2 $FASTAFILE $OUTPUTPATH
$DNAFILE1: first read DNA sequencing file, in gziped fastq format (fq.gz)
$DNAFILE2: second read DNA sequencing file, in gziped fastq format (fq.gz)
$RNAFILE1: first read RNA sequencing file, in gziped fastq format (fq.gz)
$RNAFILE2: second read RNA sequencing file, in gziped fastq format (fq.gz)
$FASTAFILE: base sequence file in fasta format (ATGC sequence)
$OUTPUTPATH: all output files will be written here, empty file folder is recommended
var.count: cleaved read number of each variant, total number of each variant in the input DNA-seq library
var.ra: organized relative activity of each variant
var.pos.ra: organized relative activity of all mutants of each position pair
pred.mtx: ps score matrix
pred.ss: 100 predicted secondary structure in the bracket format with a consensus prediction
Zhang et al. eLife 2023;13:RP90254. DOI: https://doi.org/10.7554/eLife.90254