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there are some kinds of plants, and we have some DNA-sequence data (".fastq" files) for each kind, and we plan to do the differential expression analysis bewtween these plants by R. But I am a new guy in this field, any suggestion about how to do that ?

zx8754
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user440446
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    Please read the info about [how to ask a good question](http://stackoverflow.com/help/how-to-ask) and how to give a [reproducible example](http://stackoverflow.com/questions/5963269). This will make it much easier for others to help you. – zx8754 Jan 16 '17 at 07:33

1 Answers1

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You should read documentation for edgeR:

  1. Align your reads with something like STAR or TopHat2
  2. Use HTSeq-Count with a reference annotation to generate a count matrix
  3. Give the counts to edgeR, which will do differential test

EDIT:

http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

See section 4.2 for an example.

ABCD
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    @user440446 Please consider to accept the answer if you think it's useful. You should see a tick that you can click. – ABCD Jan 16 '17 at 08:10