sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data

Autor: Pogorelcnik, Romain, Vaury, Chantal, Pouchin, Pierre, Jensen, Silke, Brasset, Emilie
Přispěvatelé: Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique, Reproduction et Développement (GReD ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: Mobile DNA
Mobile DNA, BioMed Central, 2018, 9 (1), ⟨10.1186/s13100-018-0130-7⟩
Mobile DNA, BioMed Central, 2018, 9, pp.25. ⟨10.1186/s13100-018-0130-7⟩
Mobile DNA, Vol 9, Iss 1, Pp 1-6 (2018)
Mobile DNA, 2018, 9, pp.25. ⟨10.1186/s13100-018-0130-7⟩
ISSN: 1759-8753
Popis: Background The 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. Results Here 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. Conclusions sRNAPipe 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. Electronic supplementary material The online version of this article (10.1186/s13100-018-0130-7) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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