I am currently working on downstream analysis of my RNAseq data. I have been using stringtie and its prepDE.py to extract the reads for DESeq2 for DE. Basically following http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual. And also thinking of comparing DE with edgeR.
I came across a tutorial (https://github.com/griffithlab/rnaseq_tutorial/wiki/Expression), where they ran htseq-count on alignments instead to produce raw counts for edgeR.
I read questions in forum saying the two outputs are different.
So, my question is: which reads do I use?