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Welcome to the RNA_Editing_Detection_Pipeline wiki!

Usage:

Download Reference Data

1. Create a tab-delimited file containing the urls to all required reference data keeping the first column identical to the example.

Example reference_data.txt:

genome  ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/GRCh37_mapping/GRCh37.primary_assembly.genome.fa.gz
genome_annotation       ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/GRCh37_mapping/gencode.v30lift37.annotation.gtf.gz
strand_detection        https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/hg19_RefSeq.bed.gz
rmsk    http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
dbSNP   http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp151.txt.gz
rediportal_db   http://srv00.recas.ba.infn.it/webshare/rediportalDownload/table1_full.txt.gz

2. Run get_reference_data.py to download all required data into specified directory.

Parameters:

• -i or --input: path to tab-delimited file containing data urls
• -o or --output: path to output directory

Example:

nohup python3 get_reference_data.py -i reference_data.txt -o output_path &

Index Genome for STAR

1. Run index_genome_STAR.py to index the genome for STAR.

Parameters:

• -f or --fasta: path to genome fasta file
• -a or --gtf_annotation: path to genome gtf annotation
• -o or --output: path to output directory

Example:

nohup python3 index_genome_STAR.py -f genome.fa -a annotation.gtf -o index_output/ &

Retrieve Fastq Files from SRA

1. Create a txt file containing a list of SRA accession numbers.
2. Run get_SRA_data.py to download data

Parameters:

• -a or --acc_list: path to file containing list of SRA accession numbers
• -o or --output: path to output directory

Example:

nohup python3 get_SRA_data.py -a acc.txt -o output_path &

Trim RNAseq Reads

1. Run fastp.py to trim RNAseq Reads

Parameters:

• -se or --single_end: include at beginning of parameters if data is single end
• -f or --fastq_dir: path to fastq directory
• -o or --output: path to output directory

Example:

PE data

nohup python3 fastp.py -f fastq_dir -o output_dir &

SE data

nohup python3 fastp.py -se -f fastq_dir -o output_dir &

Align RNAseq Reads

1. Make sure genome has been indexed for STAR
2. Run align_STAR.py to align paired-end data to the genome

Parameters:

• -f or --fastq_dir: path to directory containing fastq files
• -g or --genome_idx: path to STAR genome index
• -o or --output: path to output directory

Example:

nohup python align_STAR.py -f fastq_dir -g genome_index -o output_dir &

Download Fastq Files of WGS from SRA

1. Create a txt file containing a list of ERR accession numbers.
2. Run get_WGS_data.py to download data

Parameters:

• -a or --acc_list: path to file containing list of SRA accession numbers
• -o or --output: path to output directory

Example:

nohup python3 get_WGS_data.py -a acc.txt -o output_path &