Package: rockhopper (2.0.3+dfsg2-4)

[ Source: rockhopper  ]

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
 * Visualizing results in a genome browser

Other Packages Related to rockhopper

• dep: default-jre

  Standard Java or Java compatible Runtime

• dep: igv

  Integrative Genomics Viewer

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Architecture	Package Size	Installed Size	Files
all	585.3 kB	653.0 kB	[list of files]