Hi,
I am trying to perform a gene expression analysis of a FeatureCounts file using the DESeq2 tool.
I have no problem up to FeatureCounts, but when I do DESeq, which file should I use for ‘Factor level’ → ‘Count file’? I am not sure.
Please let me know if you know of any.
Welcome, @Mina
Featurecounts is one tool that produces the count files that can be used with Bioconductor differential expression tools such as DESeq2, EdgeR, and Limma.
So, in short – the outputs of Featurecounts are what you have already – and are the “count files”.
For examples, scroll down on the tool form. Right above where you clicked through to this forum, there are links to the tutorials we have that include this exact tool.
Quote from the form
Tutorials
There are 5 tutorials available which use this tool. These tutorials include training for the current version of the tool. View all tutorials referencing this tool.
Tutorials available in 1 category
Transcriptomics (5)
This is also a good place to learn which training “category” (or categories) the tool is included in, since that helps when navigating the training site to learn about methods that may not include this tool, but are still potential analysis paths. As an example, this is the direct link to the Transcriptomics category.
Related Q&A at this forum can be found under these tags → deseq2 transcriptomics featurecounts
Hope this helps but you can explain more if I am misunderstanding your question. 