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Old 06-24-2016, 10:57 AM   #124
Location: US

Join Date: Feb 2010
Posts: 27

Hi Felix,

Thank you so much for your response!

For the question 1:
After trimming, the length of the left sequence is only 7nt but the length of the right sequence is 21nt. Obviously I want to keep the 21nt sequence and ignore the 7nt sequence because it is too short. I am not sure if I can directly run Cutadapt using -g option to keep the 21nt sequence instead of 7nt sequence.

For the question 2:
Sure, a single N cannot make a difference for mapping. But for miRNA seq alignment, it is better to remove the unknown nucleotides before alignment because of the sensitivity.
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