.TH ROCKHOPPER 1 "February 2022"

.SH NAME
rockhopper \- system for analyzing bacterial RNA-seq data (command line tool)

.SH SYNOPSIS
\fBrockhopper\fP
.RI [ options ]

.SH DESCRIPTION
\fBrockhopper\fP 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).

.SH REQUIRED ARGUMENTS
.TP
.BR \fIexp1A.fastq,exp1B.fastq,exp1C.fastq\fR\ \fIexp2A.fastq,exp2B.fastq\fR
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 '%')

.SH 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.
.TP
.BR \-g\ <DIR1,DIR2>
a comma separated list of directories, each containing a genome file (*.fna), gene file (*.ptt), and rna file (*.rnt)

.SH OPTIONAL ARGUMENTS FOR EITHER REFERENCE BASED ASSEMBLY OR DE NOVO ASSEMBLY
.TP
.BR \-c\ <boolean>
reverse complement single-end reads (default is false)
.TP
.BR \-ff,\ \-fr,\ \-rf,\ \-rr
orientation of two mate reads for paired-end read, f=forward and r=reverse_complement (default is fr)
.TP
.BR \-d\ <integer>
maximum number of bases between mate pairs for paired-end reads (default is 500)
.TP
.BR \-a\ <boolean>
identify 1 alignment (true) or identify all optimal alignments (false), (default is true)
.TP
.BR \-p\ <integer>
number of processors (default is self-identification of processors)
.TP
.BR \-e\ <boolean>
compute differential expression for transcripts in pairs of experimental conditions (default is true)
.TP
.BR \-s\ <boolean>
RNA-seq experiments are strand specific (true) or strand ambiguous (false), (default is true)
.TP
.BR \-L\ <comma\ separated\ list>
labels for each condition
.TP
.BR \-o\ <DIR>
directory where output files are written (default is Rockhopper_Results/)
.TP
.BR \-v\ <boolean>
verbose output including raw/normalized counts aligning to each gene (default is false)
.TP
.BR \-SAM
output a SAM format file
.TP
.BR \-TIME
output time taken to execute program

.SH OPTIONAL ARGUMENTS FOR REFERENCE BASED ASSEMBLY ONLY
.TP
.BR \-m\ <number>
allowed mismatches as percent of read length (default is 0.15)
.TP
.BR \-l\ <number>
minimum seed as percent of read length (default is 0.33)
.TP
.BR \-y\ <boolean>
compute operons (default is true)
.TP
.BR \-t\ <boolean>
identify transcript boundaries including UTRs and ncRNAs (default is true)
.TP
.BR \-z\ <number>
minimum expression of UTRs and ncRNAs, a number in range [0.0, 1.0] (default is 0.5)

.SH OPTIONAL ARGUMENTS FOR DE NOVO ASSEMBLY ONLY
.TP
.BR \-k\ <integer>
size of k-mer, range of values is 15 to 31 (default is 25)
.TP
.BR \-j\ <integer>
minimum length required to use a sequencing read after trimming/processing (default is 35)
.TP
.BR \-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
.TP
.BR \-b\ <integer>
minimum number of full length reads required to map to a de novo assembled trancript (default is 20)
.TP
.BR \-u\ <integer>
minimum length of de novo assembled transcripts (default is 2*k)
.TP
.BR \-w\ <integer>
minimum count of k-mer to use it to seed a new de novo assembled transcript (default is 50)
.TP
.BR \-x\ <integer>
minimum count of k-mer to use it to extend an existing de novo assembled transcript (default is 5)

.SH 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

.SH SEE ALSO
https://cs.wellesley.edu/~btjaden/Rockhopper/

.BR rockhoppergui (1)