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best workflow for RNA data analysis without replications

I am wondering could anyone tell me the best work flow (software) and Statistical model should I use for RNA seq data (without replications).

Thanks a lot

rna-seq
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updated by Ram Ram • written by Chao.wang2 • Chao.wang2

What are you trying to do with the RNA-seq data? If you have no replicates, you should not attempt to assess differential expression.

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updated by Ram Ram • written by Rob Rob

Thanks for your reply, actually, I want to assess the differential expression. If I can't assess differential exprssion, what else can I do with this kind of data.

Thanks

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written by Chao.wang2 • Chao.wang2

Not much, you can't really do much of the way of comparisons. You could ask whether a gene is likely expressed, or what its major isoform is, but even then any result would have the "at least in this sample" caveat applied to it.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

You can analyse this data by fold change between the groups. But the data should be normalized. Is not the best way to avaluate rnaseq, but as you dont have replicates you can validate some of most down or up regulated rnas in your data by Real Time PCR, if is possible.

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written by silas008 silas008

1 answer

The best tool you'll find is GFold, and you should obviously be very cognizant of the caveats that come with trying to draw any firm conclusions from unreplicated data (i.e., the most this is useful for is getting some target genes for replicated targeted tests).

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written by Devon Ryan Devon Ryan

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