rockhopper

require(GCModeller);

#' A system for analyzing bacterial RNA-seq data
imports "rockhopper" from "rnaseq";

A system for analyzing bacterial RNA-seq data

Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks:

• Reference based transcript assembly (When one Or more reference genomes are available)
• Aligning reads To genomes
• Assembling transcripts
• Identifying transcript boundaries And novel transcripts such As small RNAs
• De novo transcript assembly (When reference genomes are unavailable)
• Normalizing data from different experiments
• Quantifying transcript abundance
• Testing For differential gene expression
• Characterizing operon structures

References

If you make use Of Rockhopper In your work, please cite the following:

1. A computational system For identifying operons based On RNA-seq data. Brian Tjaden. Methods, 176:62-70, 2020.
2. De novo assembly Of bacterial transcriptomes from RNA-seq data. Brian Tjaden. Genome Biology, 16:1, 2015.
3. Computational analysis Of bacterial RNA-seq data. Ryan McClure, Divya Balasubramanian, Yan Sun, Maksym Bobrovskyy, Paul Sumby, Caroline A. Genco, Carin K. Vanderpool, And Brian Tjaden. Nucleic Acids Research, 41(14):e140, 2013.