![]() # -trimmomatic :run Trimmomatic to quality trim reads # necessary due to finding excessive fusion # -jaccard_clip :option, set if you have paired reads and # (see genome-guided param section under -show_full_usage_info) # -genome_guided_bam :genome guided mode, provide path to coordinate-sorted bam file. # -long_reads :fasta file containing error-corrected or circular consensus (CCS) pac bio reads # -min_contig_length :minimum assembled contig length to report # -CPU :number of CPUs to use, default: 2 # -SS_lib_type :Strand-specific RNA-Seq read orientation. # if single-end instead of paired-end, then leave the 4th column above empty. # cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq # cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq ![]() # cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq # cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq # -samples_file tab-delimited text file indicating biological replicate relationships. # -single :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: -run_as_paired ) ![]() # -right :right reads, one or more file names (separated by commas, not spaces) # -left :left reads, one or more file names (separated by commas, not spaces) # -max_memory :suggested max memory to use by Trinity where limiting can be enabled. How can I run this in parallel on a computing grid?.How do I identify the specific reads that were incorporated into the transcript assemblies?.How do I use reads I downloaded from SRA.There are too many transcripts! What do I do?.Defining a reduced 'best' transcript set and TSA submission.Miscellaneous additional functionality that may be of interest.Gene Ontology term functional category enrichments.Identifying Sequence Polymorphisms or Variants.Sample Specificity Analysis in Many Sample Comparisons.Differential Transcript or Gene Expression. ![]() Examining Resource Usage at the End of a Trinity Run.Monitoring Progress During a Trinity Run.Trinity process and resource monitoring.Genome Guided Trinity Transcriptome Assembly.Accessing Trinity on Publicly Available Compute Resources. ![]()
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