Variant calling from rnaseq
I am doing a variant calling analysis using rna seq and I feel a bit insecure sometimes, that's why I wanted to ask. Is it a robust analysis?
Also I want to try to draw conclusions by doing a differential expression analysis of genes (using GEO2r) and isoforms (I am using stringTie and ballgown). If you have any opinion about this, I would appreciate it.
Greetings from Argentina.
1 answer
You can, theoretically, identify some mutations from RNA-seq data. But RNA is not DNA, and calling mutations from DNA sequencing data is better for this purpose.
I would recommend checking out GATK's RNA-seq short variant discovery page, as well as the many Biostars threads on this topic:
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james.hawley •
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Please ask a precise question. RNA-seq is inferior to DNA-seq for variants, please see many previous threads, but will this stop you from doing it? Why isoform analysis? It's more robust to do gene level.
Ok, thank you for you time.