trimmed one more nucleotide base I want to keep
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aiminy commented
my adapter sequence is:
GATCTGAATTCAGTGGCACAGCAGTTAGG
My sequence to be trimmed is
GATCTGAATTCAGTGGCACAGCAGTTAGGGAACGCGTAAGGCTGTATAGATCTGGAATGAACTGGCC
after trimming, I expect to get:
GAACGCGTAAGGCTGTATAGATCTGGAATGAACTGGCC
but I got
AACGCGTAAGGCTGTATAGATCTGGAATGAACTGGCC
it seems besides trimming my adapter sequence, fastq-mcf also remove one more G, I used the command like the following:
fastq-mcf -S -q 0 -l 1 LC_completo.fa R2_fastq_trim12nt_qcTrimmed_MatchBlastLtrLc_Barcode_FB-P7-Rd2-LC.2 -o R2_fastq_trim12nt_qcTrimmed_MatchBlastLtrLc_Barcode_FB-P7-Rd2-LC.2_trimwithMCF-check
How to avoid this?