How to read multiple samples with DESeq2?
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4.8 years ago

Hello

I have a count file which has multiple columns, (one column for one sample). As I found, In DESeq2 we should insert count files separately.

Is it possible to insert one file with multiple columns? like below:

Gene    Sample1  Sample2

g1      22       0

g2      5        60

....

Thanks

RNA-Seq R DESeq2 • 1.8k views
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4.8 years ago

see "Starting from count matrices" in this document http://www.bioconductor.org/help/workflows/rnaseqGene/

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4.8 years ago
GenoMax 112k

Have you looked at the DESeq2 vignette (specifically section 1.3.3)?

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4.8 years ago
ivivek_ngs ★ 5.1k

DESeq2 vignette should be fine. However , it actually needs your knowledge in R rather than the tool you want to use for DE analsys or whatever your are aiming to dol.

Read the vignette well as suggested by others. Then the below guidlines should work if you understand from the vignette. Read the file in R with header=T and rownames=1. Create the colData dataframe with the condition or group you have for your experiment Then create the DESeq data object with the design. In your case it should be DESeqDataSetFromMatrix function

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