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

ABSTRACT:

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 coun

SUBMITTER: Pogorelcnik R 

PROVIDER: S-EPMC6069783 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature