Softwares required for RIC-seq analysis
Download and install STAR (v.020201) for short reads mapping from:
https://github.com/alexdobin/STAR
Download and install SAMtools (v.0.1.19) from:
https://github.com/samtools/samtools
Download and install BEDtools (v2.28.0) from:
https://github.com/arq5x/bedtools2
Download and install FastQC for quality control of sequencing reads from:
https://www.bioinformatics.babraham.ac.uk/projects/fastqc
Download and install Trimmomatic (v.0.36) for trimming adapter from:
http://www.usadellab.org/cms/?page=trimmomatic
Download and install cutadapt (v.1.15) for cropping low-complexity fragments from:
https://cutadapt.readthedocs.io/en/stable
To extract pairwise splicing site from gtf files: #step1: perl gtf_to_bed.pl gencode.v19.annotation.gtf > gencode.v19.annotation.bed #step2: perl creat_junction_bed.pl gencode.v19.annotation.bed > gencode.v19.all_exon_junction.bed This is an example bash to obtain pairwise splicing sites from genocode.v19 annotation files. These two perl scripts are also uploaded to the scripts folder.
Important:
Add these programs to the PATH environment variable.