Trinity, Bowtie, eXpress and DEGseq (SE)
This pipeline is useful for the researcher who deal with species without reference genome.
Transcriptome de novo assembly is constructed using Trinity. Reads are mapped to contigs using bowtie, and expression revel (FPKM) is calculated using eXpress. Pairwise comparison using DEGseq, extracting differential expressed genes, and clustering based on K-means is done. It adds annotation to each contigs based on blastx to Uniprot and blastn to NR and extracts significantly up regulated GO and visualize using REVIGO.
|Execution time||About a few days (20M paired-end reads[50bp+50bp])|