I analysed my RNA-seq data for S. pombe once with Tuxedo pipeline and once with DESeq! Surprisingly I see one of the genes which is important for my experiment present in Tuxedo
gene_exp.diff output but not in
gene_exp.diff I get
nmt1 III:1837498-1844115 but when I look for it on pombase it has other coordination starting 1838335 and ending at 1839525 and I don't see this gene in deseq.res output at all. Am I missing something with annotations or there some other thing that I am not considering?
Your help is much appreciated.