ArticleMobile DNA2018
sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data.
Article in Mobile DNA, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries.Cell reports · 2025Article
- Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation.Plant cell reports · 2024Article
- sRNAflow: A Tool for the Analysis of Small RNA-Seq Data.Non-coding RNA · 2024Article
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
- Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries.Nature communications · 2023Article
- The Small RNA Component ofPlants (Basel, Switzerland) · 2023Article
- Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.International journal of molecular sciences · 2023Article
- Preparation and processing of dried blood spots for microRNA sequencing.Biology methods & protocols · 2023Review
- Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy.Frontiers in bioinformatics · 2023Article
- ITAS: Integrated Transcript Annotation for Small RNA.Non-coding RNA · 2022Article
- stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences.Frontiers in bioinformatics · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies.F1000Research · 2022Article
- Endogenous Feline Leukemia Virus (FeLV) siRNA Transcription May Interfere with Exogenous FeLV Infection.Journal of virology · 2021Article
- Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements.Biology · 2021Review
- RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.BMC bioinformatics · 2021Article
- Conserved Small Nucleotidic Elements at the Origin of Concerted piRNA Biogenesis from Genes and lncRNAs.Cells · 2020Article
- Article
- The RNA workbench 2.0: next generation RNA data analysis.Nucleic acids research · 2019Article
- Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion.Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads.
resultsHere we present a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: transposable elements, gene transcripts, microRNAs, small nuclear RNAs, ribosomal RNAs and transfer RNAs. It also provides individual mapping and counting for chromosomes, transposable elements and gene transcripts, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5'-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing counts of overlaps and corresponding z-scores.
conclusionssRNAPipe is easy to use and does not require command-line or coding knowledge. This pipeline gives quick visual and quantitative results, which are usable for publications. sRNAPipe is freely available as a Galaxy tool and via GitHub.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.