You said:

Hi,

I am doing RNA-seq analysis on plants of different stresses.

My topic is In Silico Analysis of Carotenoid Metabolism Regulatory Genes in Plants in Response to Different Developmental and Environmental Conditions. I actually couldn't figure out the processes to continue and complete my thesis research.

I searched total 8 plants Arabidopsis thalaiana (Salt stress) ,Sorghum bicolor (Drought stress) ,Glycine max(Mild drought stress), Oryza sativa japonica(Alkaline stress), Solanum tuberosum(Drought stress), Setaria viridis(Salt stress), Brachypodium distachyon(Drought stress), Hordeum vulgare(Heat stress). I uploaded genome file and annotation file in fasta and gtf .gz format together with the SRR files in fastq.gz format. I am doing it on galaxy. the pipeline I followed is fastqc, then multiqc, then trimgalore, then hisat2, then featurecounts, and deseq2.

What can I do after the step of deseq? I got featurecounts datas and deseq2 plots and results file already. Now I have left to

1. Extract Carotenoid Metabolism Genes from DEGs
2. Functional Enrichment Analysis (GO/KEGG Pathway)
3. Phylogenetic Analysis of Carotenoid Regulatory Genes
4. Motif Discovery and Conserved Domain Analysis

I am not pro in using R or ubuntu still I have to finish it in short time but got no time to learn thoroughly . what tools do I need to install and commands to run the code through R or ubuntu(wsl).