Code:
-a ADAPTER, --adapter=ADAPTER Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$' character, the adapter is anchored to the end of the read and only found if it is a suffix of the read.
As a side not too should be able to leave out the -a SEQUENCE here completely because Trim Galore should auto-detect your smallRNA adapter sequence. (but since they are the same it won't hurt I guess).
Regarding your second question the current development version has an option to remove reads with too many Ns but I am afraid it doesn't currently have the option to trim Ns from the ends of reads but if this would really help you it could add it in. Often a single N is not going to make a difference in terms of mapping, and it might in this case also change the length of the small RNA-species. So yea if you think it would be absolutely required I could add it. Best, Felix
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