Hi,

I am new to Deseq analysis. Recently i conducted metatranscriptomics analysis of bacterial community in two different conditions. My aim to explore the overall significent transcript expression and also some selective transcripts (related to specific function). I used raw featurecounts output to run Deseq and created heatmap on VSD transformed data on to 20 features.

But, due to vast number of transcripts, this does not cover my transcripts of interest. Is it ok to extract raw counts of all transcripts related to a particular function and run Deseq?

Also, the heatmap generated via vsd transformed data shows scale as -1, -0.5, 0.5 and 1.0. Are this suppossed to be the Log2F change?

This has been asked before on the support site (even within the past month) and we do not recommend running DESeq2 on a subset of transcripts or genes.

For details on the transformations, see the DESeq2 workflow.

https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#the-variance-stabilizing-transformation-and-the-rlog

For genes with high counts, both the VST and the rlog will give similar result to the ordinary log2 transformation of normalized counts