Hello guys, I am new in transcriptomic analysis. I am using tophat for mapping MACE reads (Massive analysis of 3' cDNA ends) in the wheat genome. I am analyzing salt-stressed and control samples. I have realized that some reads do map to chloroplast and mitochondrial sequences in the reference... and as far as i have understood the libraries preparation consider polyA capture. I think that I should keep this reads, but i am not really sure if its better only mapping to the nuclear genome. I want to hear more opinions, and advices and additional considerations about this issue, thank you very much for your help.
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