I have done alignment for paired-end RNA-Seq data using STAR. I now want to do differential expression analysis using the following workflow:
I have a few questions before I proceed.
1) I have generated both Unsorted and SortedByCoordinate BAM files. Which one should I use for differential expression analysis?
2) I used the option --sjdbGTFfile during alignment. Do I need to modify the downstream workflow because of this?
3) I prepared a sampleTable as suggested in workflow. It has just two columns: sample name and group (case, control). Do I need to add other details or it would be sufficient.