I want to look for polymorphisms in my mapped RNA seq data (STAR-aligned) as well as the genes they are in (and the corresponding sequences). After that I also need to isolate the sequences and compare them directly to reference cDNA sequences. What tools in Galaxy can i use for this?
To explore the transcript/gene content for RNA-seq read samples, please see → Transcriptomics / Tutorial List. The second and third listed here are good places to start (choose the option you have reference data for). The End-to-End is another full pipeline choice for when the target reference (genome/annotation) are knowns.
For variant calling, you can adapt one of these for your data → Variant Analysis / Tutorial List. Calling SNPs with a tool like Freebayes then annotating those calls with a tool like SNPeff is a common choice.
Hope this helps! 