Luis Leal, Venkat Talla, Thomas Källman, Magne Friberg, Christer Wiklund, Vlad Dincă, Roger Vila, and Niclas Backström. Molecular Ecology 27 (4), 935–48 (2018). https://doi.org/10.1111/mec.14501.

Luis Leal, Uppsala University, Uppsala, Sweden, 2017

• Filter libraries using TrimGalore
• Mask libraries using Fastq Masker
• Filter libraries using prinseq
• Filter libraries using condetri
• Screen libraries using fastQ Screen
• Reconcile paired-end libraries after using fastQ Screen (removes non-paired reads)

(Note: Index fasta files as required.)

01_quality_control.sh

(Note: Index fasta files as required.)

02_trinity_transcriptome_assembly.sh

• a. Annotate each trinity transcript using modified Trinotate protocol

03_trinotate_functional_annotation.sh

• b. Build local UniProt databases

04_build_local_UniProt_db.sh

• c. Find GO terms associated to each Trinity gene

05_associate_GO_terms_to_genes.sh

(Note: Index files as required.)

06_kallisto_transcript_quantification.sh

• a. Convert counts-per-transcript to counts-per-gene using tximport

  • a1. Associate Trinity transcript name to its gene name

  07_associate_transcript_to_gene.py

  • a2. Convert Kallisto output files from count-per-transcript to count-per-gene

  08_tximport_aggregate_transcript_counts.R

• b. Consolidate annotation file & gene counts

  09_tximport_consolidateGenes.py

10_DESeq2.R

• a. Create two-column file that lists each Trinity gene and its associated GO terms

11_gene_to_GO.py

• b. Perform gene ontology enrichment analysis

12_TopGO.R