Can anyone please let me know is there any free suitable software packages for the analysis of eukaryotic RNA-Seq data?

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Anna Liza Kretzschmar

Could you please add some more detail to your question - are you looking at eukaryotes or prokaryotes, do you have reference genes, do you have non-stressed reference transcriptome? RNA seq or microarray?

Ruhshan Ahmed Abir

You can start with looking for genes which are differentially expressed in normal sample and stress induced sample.