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trimmed one more nucleotide base I want to keep

Open aiminy opened this issue 6 years ago • 0 comments

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?

aiminy avatar Jan 29 '20 15:01 aiminy