I am sorry this question is a little bit stupid. Anyway, I need your suggestions and opinions.
When you have a stranded paired-end data and use the RSEM to get the counts, generally which method will you use? what are the advantages or disadvantages of each method?
Method 1: paired-end stranded Method 2: paired-end unstranded Method 3: R1 reads only stranded
I found the counts returned by Method 1 and 2 are quite close, and different from method 3. But when I do the differential expression analysis, the results of method 1 and method 3 do not know much difference.
Thank you very much!