Hi, i'm newbie in this forum, i'm using option -b with cutadapt to trim adapter from the fastq files , but I lose interest sequence of each reads when the adapter is in the middle or is not in a end of the read. my question is: How Cutadapt defines the cut before or after finding an adapter located in the middle of the read?. Colored sequence was removed : the command used was
cutadapt -b AGATC -o output.fastq input.fastq
1 → AGATCTGGAGGA
2 → GTGAAATAGATCCTGAAACCGTA
5 → CGAGGCGCTCGCTTCAGATCATACTAGCGTGAAAAGGTAAACACGTGCGATGAGCGGAACGTATCCAAATCTATCTAATCCACCCATCGTAGAT
I would appreciate any help.