I have RNAseq data for one sample, with two technical replicates. As I know, I need to merge them to get the gene or exon counts.
Now I get the sam files from the two techinical replicates, can I merge the sam files as: cat 1.sam 2.sam > merged.sam and then sort -k1,1 -k2,2 merged.sam?
I want to use the merged sam file for dexseq_counts.py. My sam files don't have header.. Anyone has an idea about that? Thanks..