"RNA-seq by Example" Differential Gene Expression Error
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Entering edit mode
8 weeks ago
Jeremy ▴ 740

I've been following the guidelines in "RNA-seq by Example" in order to practice analyzing RNA-seq data, but when I try to run the edger.r or deseq2.r code as follows:

Rscript code/deseq2.r

I get the following error:

Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
     cannot open file 'design.csv': No such file or directory
Execution halted

It seems that I'm missing a file called design.csv. Does anyone know what I'm doing wrong or where I can find the design.csv file?

Biostars_Handbook RNA-seq_by_Example RNA-seq • 207 views
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Entering edit mode
8 weeks ago
GenoMax 123k

You create the design.csv file using an editor in step 3 of the step-by-step process. It needs to contain the following:

sample,condition
BORED_1, bored
BORED_2, bored
BORED_3, bored
EXCITED_1, excited
EXCITED_2, excited
EXCITED_3, excited
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Entering edit mode

Got it. I missed that update. Thanks a lot!

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