## Align and estimate abundance

If assembled transcriptome sequence set and RNA-seq reads for that are available for an organism, we can align reads and estimate transcript abundance by running the script (align_and_estimate_abundance.pl) in the Trinity software package. When the Trinity package was installed using Homebrew, that script is installed in /usr/local/Cellar/trinity/2.5.1/util where 2.5.1 is the version of Trinity.

For that process, we can now use kallisto for transcript quantification in the latest version of Trinity (v2.5.1). It cannot be installed from bioconda now in macOS platform, and this version of Trinity was installed utilizing Homebrew.

Shell script to run that script is something like this.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 #!/bin/sh thre=4 transcript=IACV01.1.fsa_nt.gz left=DRR118520_1_val_1.fq.gz right=DRR118520_2_val_2.fq.gz # parameters to run above time /usr/local/Cellar/trinity/2.5.1/util/align_and_estimate_abundance.pl \ --thread_count $thre \ --transcripts$transcript \ --seqType fq \ --left $left \ --right$right \ --est_method kallisto \ --kallisto_add_opts "-t \$thre" \ --prep_reference --output_dir kallisto_out 

This command above is for paired-end sequence.