I need to reanalyse an RNA-seq experiment with 2 conditions and unfortunately no replicates. I probably don't have big changes in expression, 100-200 genes with logFC max 2-3.
I'm planning to do the the following:
- Salmon/Kallisto with a recent RefSeq collection to estimate read counts.
- tximport to import gene level counts with an offset that corrects for changes to the average transcript length across samples.
- DESeq2 with all the warnings read in the manual.
- Rank genes based on lfc, and compare it to other stuff
Any thoughts on this? Can I improve it in any way?