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)