Hi Brian. Yes, the reads have been adapter-trimmed. Moreover alignment toward long sequences (whole reference) gives good alignment rate and low while using short (miRBase) sequences.
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Originally posted by moses122 View PostI got this problem too. Did you figure out why exactly alignment is better for long sequences than miRBase?
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Originally posted by mziemann View PostPlease don't align directly to the mature.fa, only about 50% of miR reads are the exact mature sequence, you are missing a lot of sequence diversity that will map clearly to the harpin.fa. Calling 3p and 5p arm switching on the other hand, that's a different story.
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