I am new to bionformatics and working on a project and my mission is : getting the first reference transcriptom of a specie and perform differential analysis on 2 temperature conditions at isoform level on deseq2. And I have a few questions about methodology.
So far I have a reference transcritome ( I did filter my Trinity fasta according to quality redundancy and also according to transcript expression).
I am concerned it seems not recommanded to perform diffential analysis at isoform level (https://support.bioconductor.org/p/43395/#43400)
So I am wondering wether I should change tools to perform isoform level analysis, or if it is better to do a differential analysis at gene level. Also I wonder if Ihave to cluster my transcripts (using tools like corset), prior to count, since kallisto only gives count at transcript level, unless deseq2 can use the transcript id to cluster them into genes ?
And also now that I am thinking about doing an analysis at gene level I am concerned wheter my filtering according to transcript expression will skew my analysis.
Thank you for reading !