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Old 11-08-2019, 02:53 AM   #1
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Location: Italy

Join Date: Nov 2019
Posts: 2
Default Extract reads from paired-end fastq based on specific adapters with bbduk

Hello everyone, I am using (from bbmap toolkit) to extract reads from paired-end fastq files based on the presence of specific adapters in the 5' of the sequence in the "_1" fastq file.

I am using this command:

./bbmap/ -Xmx1g in1=reads_1.fastq.gz in2=reads_2.fastq.gz outm1=matched1.fastq.gz outm2=matched2.fastq.gz literal=AAACCTGAGAAACCTA k=16 hdist=0 -rcomp=f
The problem is that other that the correct reads, the output file contains also other reads which do not include the adapter sequence, es:

# from reads_1.fastq.gz
@SRR9262917.232075 232075/1

# from reads_2.fastq.gz
@SRR9262917.232075 232075/2

Does anyone know why this may be happening and how to avoid this?

Thanks in advance.
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