Introduction
This pipeline is used to generate the base-pairing map from deep mutational sequencing data of RNA ribozyme, with the method introduced in the paper "Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity".
Requirement
Before running this pipline, make sure these programs were correctly installed.
SeqPrep (https://github.com/jstjohn/SeqPrep)
python 2.7.15
unpigz 2.4
gsplit 8.29
pigz 2.4
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: uncleaved and cleaved read number of each variant
var.ra: organized relative activity of each variant
var.pos.ra: organized relative activity of all mutants of each position pair
var.msa_RA_0.5: sequence alignment of variants with relative activity higher than 0.5
pred.mtx: ps score matrix
pred.ss: 100 predicted secondary structure in the bracket format with a consensus prediction
MSA(Multiple sequence alignment) files:
cp.var.msa_RA_0.5: MSA of CPEB3 used to perform covariation analysis.
tw.var.msa_RA_0.5: MSA of CPEB3 used to perform covariation analysis.