Question: (Closed) Best way to get differential expression from a txt file of gene counts
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gravatar for wmtennant91
21 months ago by
wmtennant910 wrote:

I have a text file with gene counts from two different conditions and I would like to create a list of genes with significantly different expression levels. DESEQ2 seems like a good tool, but are there other suggestions?

rna-seq • 369 views
ADD COMMENTlink written 21 months ago by wmtennant910

Hello wmtennant91!

Please use te search function and google for differential expression tools (edgeR and limma being the other most prominent ones). There are literally dozens or even hundreds of posts and discussions on the matter which one is preferred in a given situation. Read the available resources first and come back if there are specific questions.

As a starting point: https://mikelove.wordpress.com/2016/09/28/deseq2-or-edger/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 21 months ago by GenoMax95k • written 21 months ago by ATpoint44k
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