Hi, I am working on plant Arabidopsis. I have the samples for 4 plant types (WT, KO1, KO2 and OE1) in three replicates, Mock treated and after stress treatment. So in total 24 samples (4 Mock and 4 Treated, 3 replicates of each). I would like to analyse the differential gene expression in each sample type before treatment (Mock) and after treatment. I am using STAR for alignment of the raw reads on reference genome and to output alignments translated into transcript coordinates in the Aligned.toTranscriptome.out.bam file. These files I am using for transcript quantification on RSEM. But I am getting a problem:
Cannot open /Documents/Umesh/Analysis123/star/GENOME/genome.grp! It may not exist.
So I seek help for: 1. Is this the right approch? 2. Can I use other programs for DGE analysis 3. What is the proper pipeline for this experiment? Since I am confused about so many tools. Please guide me as I am new to this kind of analysis.