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
- Extract Carotenoid Metabolism Genes from DEGs
- Functional Enrichment Analysis (GO/KEGG Pathway)
- Phylogenetic Analysis of Carotenoid Regulatory Genes
- 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).
While not "commands to run the code through R" it would be beneficial to take a look at
DESeq2
vignette that explains everything related to DE analysis: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.htmlThank you. Now I am able to get some plots as my output through R. Still learning.
Where did you copy-paste this post from? It looks like you inadvertently included something that shows that this was copy pasted.