piRNAnalyzer

piRNAnalyzer is a fully automated bash pipeline for the analysis of piRNAs in planarian small RNA Seq samples.

The piRNAnalyzer pipeline includes preprocessing of sequencing data, read mapping, annotation to genomic features, as well as quality control steps. It comes with all pre-built reference files necessary.

Setup

Required third party programs (please make sure that these are properly set up and can be invoked from the command line):

Software	Minimum version	Link	Command Line Invocation
Cutadapt	1.15	https://cutadapt.readthedocs.io/en/stable/	cutadapt
umitools	0.2.0	https://github.com/weng-lab/umitools	umitools reformat_sra_fastq
SortMeRNA	2.1	https://bioinfo.lifl.fr/RNA/sortmerna/	sortmerna
bowtie	1.2.2	http://bowtie-bio.sourceforge.net/index.shtml	bowtie
piPipes	1.5.0	https://github.com/bowhan/piPipes	piPipes_fastq_to_insert, piPipes_insertBed_to_bed2
bedtools	2.26.0	https://bedtools.readthedocs.io/en/latest/	bedtools
samtools	1.7	http://www.htslib.org/	samtools
bedGraphtoBigWig	-	https://genome.ucsc.edu/goldenpath/help/bigWig.html	bedGraphToBigWig
R	4.1.2	https://www.r-project.org/	R

Required R packages will be downloaded automatically if not already installed on the user's system.

How to use

1. Download the latest release of piRNAnalyzer and extract the zipped folder to the desired directory.
2. Copy raw data into the folder "01-Raw" within piRNAnalyzer's folder structure.
3. Invoke the bash script "piRNAnalyzer.sh".

A sample dataset is available for download at GSE192524

Command Line Options

Flag	Function
-h	print this help message
-p	set the number of processor cores to be used (default: 4)
-f	setting filter options for preprocessing (default:all)
Filter Options:	all perform all filtering steps during preprocessing rRNA only perform rRNA filtering tRNA only perform tRNA filtering none perform no additional filtering steps during preprocessing
-v	print software version

Citation

piRNAnalyzer is an automated version of the workflow presented in DOI: 10.1007/978-1-0716-3275-8_3

Pittroff A, Kim IV, Demtröder T, Kuhn CD. Genome-Wide Analysis of Planarian piRNAs. Methods Mol Biol. 2023;2680:55-65. doi: 10.1007/978-1-0716-3275-8_3. PMID: 37428370.