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

EXAMPLE:

adapter

12bp的對(duì)稱adapter

-a TGATCGGAAGAGC

-A TGATCGGAAGAGC

R1去之前

R1去之后

R2去之前

R2去之后