This serves as a repository of codes to analyze Tetraselmis sp - TetV1 metatranscriptome.
VIRUS ANALYSIS
- Trimmomatic and FastQC
- Tuxedo protocol (Genome-guided transcriptome assembly) 2a. HISAT2. RNA-seq PE read alignment. 2b. StringTie. Assembly, quantification, merge all transcripts. 2c. Ballgown. Calculate FPKM.
HOST ANALYSIS
- Bowtie2 (remove virus, TetV-1, reads)
- Trinity (de novo assembly)
- BUSCO (Chlorophyta single copy genes)
- TransRate (filter the bad assemblies)
- RSEM (Gene/Transcript quantitation)
- DESeq2 in Trinity (Differential Expression)
- TransDecoder (coding sequence identification)
- Trinotate (functional annotation)
- topGO (gene ontology enrichment)