This pipeline gives quick visual and quantitative results, which are usable for publications. SRNAPipe is easy to use and does not require command-line or coding knowledge. 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. 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. 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. Such high-throughput sequencing typically produces several millions reads. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. 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.

Galaxy sequence analysis