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)

                                          February 2022                             ROCKHOPPER(1)