Platform: NovaSeq 6000 platform, PE150
Library type: 350bp insert cDNA library (depends on peak distribution)
Sequencing strategy: Paired-End 150 bp
Recommend data amount: 2 Gb raw data/sample
(1) Sequencing data quality control: Nucleotide distribution, Base quality distribution, rRNA ratio assessment;
(2) Sequence alignment analysis: Alignment result statistics, Saturation of sequencing, Coverage of sequencing;
(3) Reference genome annotation (NR, Swiss-Prot, Pfam, COG, GO, KEGG);
(4) Expression analysis: Expression distribution (With two or more samples), Analysis of expression between samples (Venn analysis, Correlation analysis, PCA analysis);
(5) Differential expression analysis (With two or more samples);
(6) Gene set analysis: Venn analysis, Cluster analysis, Function annotation analysis (COG, GO, KEGG), Function enrichment analysis (GO, KEGG), Function enrichment chordal graph, Ipath analysis;
(7) sRNA analysis: sRNA prediction, sRNA annotation (Blast, sRNAMap, sRNATarBase, SIPHT, Rfam), sRNA secondary structure prediction, sRNA target gene prediction;
(8) Transcript structure analysis: Operon analysis, Transcription start and end sites prediction, UTR annotation and analysis, Promoter sequence prediction, SNP/InDel analysis (SNP/InDel annotation, SNP/InDel regional distribution, SNP statistics).