I am looking/have looked at its documentation but I can't find a specific reference to the tool removing N calls. Does anyone know if it does specifically do this?
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robert.murphy •
Not by default. Following is what controls the N containing reads.
maxns=-1 If non-negative, reads with more Ns than this
(after trimming) will be discarded.
You don't want to selectively remove N's from middle of reads anyway. If there are consistent N's are beginning or ends of reads then you could do a forcetrimleft= (or right) to remove a fixed number of bases.
So not is not necessary an improvement to trim Ns?
Do you have any insight as to the use of Trimmomatic "vs" BBDUK? It seems Trimmomatic default trims Ns in leading and tail bases(if called to trim leading and tail bases that is)
If you include LEADING: and TRAILING: option for trimmomatic then trimmomatic may be removing N's because they fall under a certain quality.
Adding forcetrimleft=number_of_bases_here and forcetrimright= in bbduk.sh is eliminating those bases irrespective of quality. That is a forced or hard trim. If you want to take quality into account then there are additional options in bbduk.sh that will give you finer control.
minavgquality=0 (maq) Reads with average quality (after trimming) below
this will be discarded.
maqb=0 If positive, calculate maq from this many initial bases.
minbasequality=0 (mbq) Reads with any base below this quality (after
trimming) will be discarded.
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Use cutadapt. Cutadapt filters reads based on N content (fraction of Ns) or N's from ends of the reads.