Question

Reverse Normalized RNA-seq readcounts/fpkm values to raw readcounts

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knholm • 0

@knholm-18825

Last seen 3.9 years ago

I received DESeq2 normalized readcount and FPKM values from our experiment, but the files containing our raw read counts are not present.

I need the raw readcount values, and was wondering if there is any way to reverse the values from normalized to raw?

RNA-seq deseq2 normalization readcount reverse • 1.2k views

ADD COMMENT • link updated 5.9 years ago by Michael Love 42k • written 5.9 years ago by knholm • 0

score 0 · Answer 1 · 2018-12-13

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Michael Love 42k

@mikelove

Last seen 21 hours ago

United States

There's not a good reason to do this if its your own experiment. The original data very likely exists, and someone should be able to help you access it. If not, it's really not that hard to regenerate the counts. The best pipelines can take about 3-5 minutes per sample to generate counts for DESeq2.

ADD COMMENT • link 5.9 years ago Michael Love 42k

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Thanks Michael,

Unfortunately our raw data was deleted off the server, which is why I can't access it. And I would like to re-run the analysis through EdgeR, because the analysis performed by the sequencing company with DESeq2 appears to be missing some genes that we feel are significantly differentially expressed by our calculations of readcount, although I want to adjust for FDR using appropriate algorithms.

Do you know where I can find these pipelines for reversing normalization?

ADD REPLY • link 5.9 years ago knholm • 0

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No I don't have a recommendation for this.

ADD REPLY • link 5.9 years ago Michael Love 42k