Protocol of cutadapt

Question

[gufernandez10]

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?. Hihlighted sequence was removed : the command used was

cutadapt -b AGATC -o output.fastq input.fastq

1 -> AGATCTGGAGGA
_____^---^
2 -> GTGAAATAGATCCTGAAACCGTA
____________^---^
3 -> AGCGGAGTGAAATAGATCCTGAAACCGTATGCTCTAGTCTTGTGACGA
__________________^---^
4 -> CGCAGAACAGAGCGTGCATAACGACTGAAAAGCGACGCAGATCAAAGTGGAAGATGTACTGTTTGCGATGGTGAAAGAAGTAGAAAATCGCCCAGCTGTT
___________________________________________^---^
5 -> CGAGGCGCTCGCTTCAGATCATACTAGCGTGAAAAGGTAAACACGTGCGATGAGCGGAACGTATCCAAATCTATCTAATCCACCCATCGTAGAT
____________________^---^
6 -> CACTTGAACTCCGCCATCTCCGTTACTTCATCACAGTGGCTGAAGATCTGCATTTCAGCCGCGCGGCAGAGC
________________________________________________^---^

I would appreciate any help.

[PoGibas]

Why you use option b, instead of a or g? Are your adapters in 5' or 3' ends of reads?

[gufernandez10]

hi, yes, some adapters and contaminants appearing in different parts of the reads, i identifies some contaminants with fastqc.

[PoGibas]

To answer your question: "How Cutadapt defines the cut?".

Cutadapt states this very clearly: "The adapter itself and anything that follows is trimmed".

But are your using right tool do achieve wanted results? cutadapt removes adapters and if you want to remove contaminants you might want to use another tool.