Hi every one
I received some paired end reads containing specific Lexogen primers. So before assembly the primers must be removed from the reads. According to Lexogen protocol I must remove 9 nucleotides from 5' side of R1 and 6 nucleotides from 3' side of of R2. Is there any especial command in BBMap or any other software to accomplish this kind of trimming? In BBMap I just found command for removal specific number of nucleotides from tail of a read but for 5' side of the read I could not find a command as well. Would you please guide me to trim my reads?
I received some paired end reads containing specific Lexogen primers. So before assembly the primers must be removed from the reads. According to Lexogen protocol I must remove 9 nucleotides from 5' side of R1 and 6 nucleotides from 3' side of of R2. Is there any especial command in BBMap or any other software to accomplish this kind of trimming? In BBMap I just found command for removal specific number of nucleotides from tail of a read but for 5' side of the read I could not find a command as well. Would you please guide me to trim my reads?
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