how to analyse differential gene expression for denovo data

I am analyzing 4 SRA accessions having transcriptome libraries of two control and two disease conditions for plant samples which have no reference genome yet. I want to calculate differential gene expression from them.

  1. SRX13450302 ---- R1 diseased
  2. SRX13450301 ----R2 diseased
  3. SRX13450300 ---- R1 Control
  4. SRX13450299 ----- R2 Control

Can anyone provide support to do analysis as I tried many times on galaxy server but the job failed. please help me out.

Hi @Anand_Mishra

This related Q&A has tutorial links with an exact process Differentially expressed genes

Also here

More choices:

  1. If you are not familiar with Galaxy, start with a few “Introduction to Galaxy Analysis” tutorials first then progress to domain specific tutorials for the topic “Transcriptomics”.
  2. Try running through these with the tutorial data to learn the analysis process. Then, run the analysis on your own data. Most tutorials have an associated workflow that can be imported and used directly or customized.
  3. You can ask for help troubleshooting errors at this forum.