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Trinity

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General Description

Trinity version r20140717

Basic Usage

module load bio/#to load all bio modules
module load bio/trinity/r20140717 #to load trinity alone

Useful Options

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#
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#
# Required:
#
#  --seqType <string>      :type of reads: ( fa, or fq )
#
#  --JM <string>            :(Jellyfish Memory) number of GB of system memory to use for 
#                            k-mer counting by jellyfish  (eg. 10G) *include the 'G' char 
#
#  If paired reads:
#      --left  <string>    :left reads, one or more (separated by space)
#      --right <string>    :right reads, one or more (separated by space)
#
#  Or, if unpaired reads:
#      --single <string>   :single reads, one or more (note, if single file contains pairs, can use flag: --run_as_paired )
#
####################################
##  Misc:  #########################
#
#  --SS_lib_type <string>          :Strand-specific RNA-Seq read orientation.
#                                   if paired: RF or FR,
#                                   if single: F or R.   (dUTP method = RF)
#                                   See web documentation.
#
#  --CPU <int>                     :number of CPUs to use, default: 2
#  --min_contig_length <int>       :minimum assembled contig length to report
#                                   (def=200)
#
#  --genome <string>               :genome guided mode, provide path to genome fasta file (see genome-guided param section under --show_full_usage_info)
#
#  --jaccard_clip                  :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.)
#
#  --trimmomatic                   :run Trimmomatic to quality trim reads
#                                        see '--quality_trimming_params' under full usage info for tailored settings.
#                                  
#
#  --normalize_reads               :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.
#     
#
#  --output <string>               :name of directory for output (will be
#                                   created if it doesn't already exist)
#                                   default( your current working directory: "/afs/crc.nd.edu/group/genomics/yoda/vakulenko/trimmed/sam/bam/individualbams/testmergevcf/trinity_out_dir" )
#  
#  --full_cleanup                  :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
#
#  --cite                          :show the Trinity literature citation
#
#  --version                       :reports Trinity version (trinityrnaseq_r20140717) and exits.
#
#  --show_full_usage_info          :show the many many more options available for running Trinity (expert usage).

###############################################################################
#
#  *Note, a typical Trinity command might be:
#
#        Trinity --seqType fq --JM 100G --left reads_1.fq  --right reads_2.fq --CPU 6
#
#
#    and for Genome-guided Trinity:
#
#        Trinity --genome genome.fasta 
#                --genome_guided_max_intron 10000 --genome_guided_sort_buffer 10G 
#                --genome_guided_CPU 4 
#                --seqType fq --JM 2G --left reads_1.fq  --right reads_2.fq --CPU 6
#                (and optionally provide your own bam file: --genome_guided_use_bam rnaseq_alignments.csorted.bam 
#                 or Trinity will run GSNAP to generate one. )
#
#
#     see: /afs/crc.nd.edu/x86_64_linux/bio/trinity/r20140717/sample_data/test_Trinity_Assembly/
#          for sample data and 'runMe.sh' for example Trinity execution
#     For more details, visit: http://trinityrnaseq.sf.net
#
###############################################################################

Further Information

See the official website: Babraham Bioinformatics