###record Chlamydomonas reinhardtii RNA_seq analysis procedure #First--quality control and filter: raw data -> clean data (need softwares containing FastP or combination of FastQC and Trimmomatic)
#second--alignment(reference, but no reference need transcriptome assembled de novo by Trinity): downloading reference genome from Phytozome website, and then aligning clean data to reference genome (softwares: STAR, attention :u should create genome index before alignment; hisat2; subread; bowtie2, and so on)
#third--expression quatification: need second procedure result file like .BAM file, get genes level or transcripts level reads count ( software: featureCounts), other key points: Samples similarity detection, method: PCA analysis(scikit-learn ) and relation analysis (scipy)
#fourth--differential genes analysis: hunting for differential genes at comprision between control group and test group (software: edger ; DEseq2)
#fifth and more--enrichment including GO and KEGG analysis and more(GO enrichment analysis: need TopGO or GOstat ,and clusterprofile, the last two softwares can also be available on Kegg enrichment anaysis)
#others--more details analysis: WGCNA analysis (need phenotype data or metabolomics data); GSEA analysis ; specials genes relationship analysis ;genes category anaysis ; and more