Transcriptome analysis of virus infected plants and their controls

Question

[diya]

My treatments are two genotypes: susceptible ("sus") and resistant ("res") when infected with virus and their controls, a total of 4 treatments. Transcriptome data is compared in four combinations, sus-infected vs control, res-infected vs control, sus-infected vs res-infected and sus-control vs res-control. In the comparison they gave transcript ids and gene ids but all transcripts are not identified with gene id; Why? Can I take transcripts as differentially expressed transcripts and gene as DEG's.

I have to draw heatmaps for few DEG's involved in different pathways of defense what should I follow any software for heatmap? Any suggestions please? Stuck with this for months

[Ram]

You're stuck for months looking for heatmap software? I find that hard to believe.

[diya]

iam not all related biotechnology or bioinformatics, none of my seniors or guides have done any work related to this, not even realtime PCR or gene related works.

[manaswwm]

I think the majority of people usually go with genes for transcriptomics analysis (choose a representative transcript per gene) because it is easier to do downstream analysis. So I would personally first find out a way of choosing a representative transcript per gene.

Heatmaps are easier to make given that you have the foldchange of the genes that you want to visualize. You can check out pheatmap package (if you are using R), there are many nice tutorials like this first google hit. If you are a newbie then I would recommend you to just follow the tutorial as is before trying to implement this on your data