RNA-seq workflow

[foxyg]

Is there a standard RNA-seq workflow like DNA-sequencing?

I guess my question is the GATK steps such as realignement, recalibrate, would those work on RNA-seq data?

Thanks

[shurjo]

Is there a standard RNA-seq workflow like DNA-sequencing?

I guess my question is the GATK steps such as realignement, recalibrate, would those work on RNA-seq data?

Thanks

If you want to thinks in terms of formalized workflows like GATK, there are a couple of options with RNA-Seq data. Two that come to mind are the TopHat/Cufflinks/myRNA suite and the htseq Python framework. Depending on what your final needs are and your level of comfort with programming, you could also string together different open-source tools into your own custom pipeline.