---
name: "rockhopper"
section: "1"
platform: "linux"
package: "rockhopper"
version: "2.0.3+dfsg2-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/rockhopper"
---

# rockhopper(1)

system for analyzing bacterial RNA-seq data (command line tool)

## NAME

rockhopper - system for analyzing bacterial RNA-seq data (command line tool)

## SYNOPSIS

**rockhopper** \[*options*\]

## DESCRIPTION

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

## REQUIRED ARGUMENTS

- ***exp1A.fastq,exp1B.fastq,exp1C.fastq* *exp2A.fastq,exp2B.fastq***

  a comma separated list of sequencing files (in FASTQ, QSEQ, FASTA, SAM, or BAM format) for replicate experiments, one list per experimental condition (mate-pair files should be delimited by '%')

## REFERENCE BASED ASSEMBLY VS. DE NONO ASSEMBLY

If the -g option is used, then rockhopper aligns reads to one or more reference genomes, otherwise, rockhopper performs de novo transcript assembly.

- **-g \<DIR1,DIR2\>**

  a comma separated list of directories, each containing a genome file (\*.fna), gene file (\*.ptt), and rna file (\*.rnt)

## OPTIONAL ARGUMENTS FOR EITHER REFERENCE BASED ASSEMBLY OR DE NOVO ASSEMBLY

- **-c \<boolean\>**

  reverse complement single-end reads (default is false)

- **-ff, -fr, -rf, -rr**

  orientation of two mate reads for paired-end read, f=forward and r=reverse\_complement (default is fr)

- **-d \<integer\>**

  maximum number of bases between mate pairs for paired-end reads (default is 500)

- **-a \<boolean\>**

  identify 1 alignment (true) or identify all optimal alignments (false), (default is true)

- **-p \<integer\>**

  number of processors (default is self-identification of processors)

- **-e \<boolean\>**

  compute differential expression for transcripts in pairs of experimental conditions (default is true)

- **-s \<boolean\>**

  RNA-seq experiments are strand specific (true) or strand ambiguous (false), (default is true)

- **-L \<comma separated list\>**

  labels for each condition

- **-o \<DIR\>**

  directory where output files are written (default is Rockhopper\_Results/)

- **-v \<boolean\>**

  verbose output including raw/normalized counts aligning to each gene (default is false)

- **-SAM**

  output a SAM format file

- **-TIME**

  output time taken to execute program

## OPTIONAL ARGUMENTS FOR REFERENCE BASED ASSEMBLY ONLY

- **-m \<number\>**

  allowed mismatches as percent of read length (default is 0.15)

- **-l \<number\>**

  minimum seed as percent of read length (default is 0.33)

- **-y \<boolean\>**

  compute operons (default is true)

- **-t \<boolean\>**

  identify transcript boundaries including UTRs and ncRNAs (default is true)

- **-z \<number\>**

  minimum expression of UTRs and ncRNAs, a number in range \[0.0, 1.0\] (default is 0.5)

## OPTIONAL ARGUMENTS FOR DE NOVO ASSEMBLY ONLY

- **-k \<integer\>**

  size of k-mer, range of values is 15 to 31 (default is 25)

- **-j \<integer\>**

  minimum length required to use a sequencing read after trimming/processing (default is 35)

- **-n \<integer\>**

  size of k-mer hashtable is ~ 2^n (default is 25). HINT: should normally be 25 or, if more memory is available, 26. WARNING: if increased above 25 then more than 1.2M of memory must be allocated

- **-b \<integer\>**

  minimum number of full length reads required to map to a de novo assembled trancript (default is 20)

- **-u \<integer\>**

  minimum length of de novo assembled transcripts (default is 2\*k)

- **-w \<integer\>**

  minimum count of k-mer to use it to seed a new de novo assembled transcript (default is 50)

- **-x \<integer\>**

  minimum count of k-mer to use it to extend an existing de novo assembled transcript (default is 5)

## EXAMPLES

reference based assembly with single-end reads\
         % rockhopper \<options\> -g genome\_DIR1,genome\_DIR2 aerobic\_replicate1.fastq,aerobic\_replicate2.fastq anaerobic\_replicate1.fastq,anaerobic\_replicate2.fastq

de novo assembly with single-end reads\
         % rockhopper \<options\> aerobic\_replicate1.fastq,aerobic\_replicate2.fastq anaerobic\_replicate1.fastq,anaerobic\_replicate2.fastq

## SEE ALSO

https://cs.wellesley.edu/~btjaden/Rockhopper/

[**rockhoppergui**(1)](/rockhoppergui/1.md)