.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.44.1.
.TH TRINITY "1" "February 2015" "Trinity version: Trinity_v2.0.2" "User Commands"
.SH NAME
Trinity \- RNA-Seq De novo Assembly
.SH DESCRIPTION
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads. Trinity partitions
the sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at a given gene or locus, and then processes
each graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.
.SH OPTIONS
Required:
.IP
\fB\-\-seqType\fR <string>
type of reads: ( fa, or fq )
.IP
\fB\-\-max_memory\fR <string>
suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
provied in Gb of RAM, ie.  '\-\-max_memory 10G'
.P
If paired reads:
.IP
\fB\-\-left\fR  <string>
left reads, one or more (separated by space)
.IP
\fB\-\-right\fR <string>
right reads, one or more (separated by space)
.P
Or, if unpaired reads:
.IP
\fB\-\-single\fR <string>
single reads, one or more (note, if single file contains pairs, can use flag: \fB\-\-run_as_paired\fR )
.P
Misc:
.IP
\fB\-\-SS_lib_type\fR <string>
Strand\-specific RNA\-Seq read orientation.
if paired: RF or FR,
if single: F or R.   (dUTP method = RF)
See web documentation.
.IP
\fB\-\-CPU\fR <int>
number of CPUs to use, default: 2
.IP
\fB\-\-min_contig_length\fR <int>
minimum assembled contig length to report (def=200)
.IP
\fB\-\-long_reads\fR <string>
fasta file containing error\-corrected or circular consensus (CCS) pac bio reads
.IP
\fB\-\-genome_guided_bam\fR <string>
genome guided mode, provide path to coordinate\-sorted bam file.
(see genome\-guided param section under \fB\-\-show_full_usage_info\fR)
.IP
\fB\-\-jaccard_clip\fR
option, set if you have paired reads and
you expect high gene density with UTR
overlap (use FASTQ input file format
for reads).
(note: jaccard_clip is an expensive
operation, so avoid using it unless
necessary due to finding excessive fusion
transcripts w/o it.)
.IP
\fB\-\-trimmomatic\fR
run Trimmomatic to quality trim reads
see '\-\-quality_trimming_params' under full usage info for tailored settings.
.IP
\fB\-\-normalize_reads\fR
run in silico normalization of reads. Defaults to max. read coverage of 50.
see '\-\-normalize_max_read_cov' under full usage info for tailored settings.
.IP
\fB\-\-no_distributed_trinity_exec\fR
do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
.IP
\fB\-\-output\fR <string>
name of directory for output (will be
created if it doesn't already exist)
default(your current working directory)
.IP
\fB\-\-full_cleanup\fR
only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
.IP
\fB\-\-cite\fR
show the Trinity literature citation
.IP
\fB\-\-version\fR
reports Trinity version (Trinity_v2.0.2) and exits.
.IP
\fB\-\-show_full_usage_info\fR
show the many many more options available for running Trinity (expert usage).
.SH EXAMPLES
A typical Trinity command might be:
.IP
Trinity \fB\-\-seqType\fR fq \fB\-\-max_memory\fR 50G \fB\-\-left\fR reads_1.fq  \fB\-\-right\fR reads_2.fq \fB\-\-CPU\fR 6
.P
and for Genome\-guided Trinity:
.IP
Trinity \fB\-\-genome_guided_bam\fR rnaseq_alignments.csorted.bam \fB\-\-max_memory\fR 50G
        \fB\-\-genome_guided_max_intron\fR 10000 \fB\-\-CPU\fR 6
.SH "SEE ALSO"
see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
for sample data and 'runMe.sh' for example Trinity execution
.P
For more details, visit: http://trinityrnaseq.github.io