.. _backbone-label:

#########
 Trinity
#########

**************
 Introduction
**************

Trinity assembles transcript sequences from Illumina RNA-Seq data.

**********
 Versions
**********

-  2.15.0
-  2.15.1

**********
 Commands
**********

-  abundance_estimates_to_matrix.pl
-  ace2sam
-  align_and_estimate_abundance.pl
-  analyze_blastPlus_topHit_coverage.pl
-  analyze_diff_expr.pl
-  blast2sam.pl
-  bowtie
-  bowtie2
-  bowtie2-build
-  bowtie2-inspect
-  bowtie2sam.pl
-  contig_ExN50_statistic.pl
-  define_clusters_by_cutting_tree.pl
-  export2sam.pl
-  extract_supertranscript_from_reference.py
-  filter_low_expr_transcripts.pl
-  get_Trinity_gene_to_trans_map.pl
-  insilico_read_normalization.pl
-  interpolate_sam.pl
-  jellyfish
-  novo2sam.pl
-  retrieve_sequences_from_fasta.pl
-  run_DE_analysis.pl
-  sam2vcf.pl
-  samtools
-  samtools.pl
-  seq_cache_populate.pl
-  seqtk-trinity
-  sift_bam_max_cov.pl
-  soap2sam.pl
-  tabix
-  trimmomatic
-  Trinity
-  Trinity_gene_splice_modeler.py
-  TrinityStats.pl
-  wgsim
-  wgsim_eval.pl
-  zoom2sam.pl

*************
 Example job
*************

Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=trinity     # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load trinity/XXXX       ### Latest version is recommended.