cutadapt

For paired-end reads:

cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq

-a ADAPTER, --adapter=ADAPTER

                        Sequence of an adapter ligated to the 3' end (paired

                        data: of the first read). The adapter and subsequent

                        bases are trimmed. If a '$' character is appended

                        ('anchoring'), the adapter is only found if it is a

                        suffix of the read.

-A ADAPTER 3' adapter to be removed from second read in a pair.

-e ERROR_RATE, --error-rate=ERROR_RATE

                        Maximum allowed error rate (no. of errors divided by

                        the length of the matching region). Default: 0.1

-q [5'CUTOFF,]3'CUTOFF, --quality-cutoff=[5'CUTOFF,]3'CUTOFF

                        Trim low-quality bases from 5' and/or 3' ends of each

                        read before adapter removal. Applied to both reads if

                        data is paired. If one value is given, only the 3' end

                        is trimmed. If two comma-separated cutoffs are given,

                        the 5' end is trimmed with the first cutoff, the 3'

                        end with the second.

-j CORES 10

-q --quality-cutoff  15

-m LENGTH, --minimum-length=LENGTH

                        Discard reads shorter than LENGTH. Default: 0

我理解的去adapter

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EXAMPLE:

adapter

12bp的对称adapter

-a TGATCGGAAGAGC

-A TGATCGGAAGAGC

R1去之前 R1去之后 R2去之前 R2去之后