Question: What is the right illumina universal adapter sequence for trimming paired-end reads?
1
gravatar for maria2019
10 months ago by
maria201980
maria201980 wrote:

I have paired-end WES reads and FastQC report shows adapter content error “Illumina Universal adaptor”. I read the Adapter_list.txt in the fastQC folder which says that the Illumina universal adapter can be summarized in the 12 bp fragment of AGATCGGAAGAG.

My question is should I use this sequence (AGATCGGAAGAG) for both forward and reverse reads? or I should make a complementary sequence of CTCTTCCGATCT for the reverse read?

cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -o tr_R1.fastq -p tr_R2.fastq R1.fastq R2.fastq

or

cutadapt -a AGATCGGAAGAG -A CTCTTCCGATCT -o tr_R1.fastq -p tr_R2.fastq R1.fastq R2.fastq

?

fastqc wes trimadaptor • 2.9k views
ADD COMMENTlink modified 10 months ago by lakhujanivijay4.7k • written 10 months ago by maria201980
0
gravatar for lakhujanivijay
10 months ago by
lakhujanivijay4.7k
India
lakhujanivijay4.7k wrote:

The answer is

cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -o tr_R1.fastq -p tr_R2.fastq R1.fastq R2.fastq

You can use the same sequence. I think you should also check the trimming report, read 1 and read 2 should have similar stats.

ADD COMMENTlink written 10 months ago by lakhujanivijay4.7k

Thank you for your answer. I have tried both ways and then I see a good fastQC result with either of them! That is why I am not sure if I should just keep the first one or dig into it and find out which one is better.

What would be the good comparison point to decide which one to use?

ADD REPLYlink modified 10 months ago • written 10 months ago by maria201980

can you post the fastqc images here?

ADD REPLYlink written 10 months ago by lakhujanivijay4.7k

Does cutadapt remove the sequence you put in and its reverse complement (+ to the end of the read) from every string in the fastq file?

ADD REPLYlink written 9 months ago by cristian240
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