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Old 11-11-2010, 12:09 PM   #1
foxyg
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Default RNA-seq workflow

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
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Old 11-11-2010, 04:26 PM   #2
shurjo
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Quote:
Originally Posted by foxyg View Post
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.
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