RNA-seq for DGE
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amy16 • 0
@amy16-14425
Last seen 5.8 years ago

I have got RNA-seq reads from Illumina which I've trimmed adapters using trimmomatic and then aligned it with reference genome using hisat2. Now I've run through string tie for transcript identification and quantification. I would like to use ballgown for differential gene expression determination. Please advise if the pipeline I 've followed so far is right. also, I would like to use Ballgown for differential gene expression determination. Can anyone advise me on a good documentation for ballgown usage?

 

stringtie illumina hisat2 ballgown • 1.5k views
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@kvittingseerup-7956
Last seen 11 months ago
European Union

Your apporach sounds good although a few details are lacking to really judge it. I would suggest you take a look at stringtie's homepage where they make a nice outline including links to Ballgown usage.

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