TS-like ribozyme

Introduction

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.

Requirement

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

Usage

bash run.sh $DNAFILE1 $DNAFILE2 $RNAFILE1 $RNAFILE2 $FASTAFILE $OUTPUTPATH

Arguments:

$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

Outputs:

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

Reference:

Zhang et al. eLife 2023;13:RP90254. DOI: https://doi.org/10.7554/eLife.90254