Hi folks,
I am trying to do adapter and low quality trimming of a fungal genome (prepared with Illumina DNA nano kit and sequenced with HiSeq 2000 100PE). After using BBduk to trim adapters and low quality reads as following
>./bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1_q25.fastq.gz out2=R2_q25.fastq.gz ktrim=r k=21 mink=11 hdist=2 tpe tbo ref=resources/adapters.fa qtrim=rl trimq=25
Still FASTQC showed a K-mer content warning for both R1 and R2 reads [ https://goo.gl/photos/Lsyt7YJeQnjB8HQq5 ]. Can I have your opinion how shall I handle my data? Shall I just remove the first 20 bases to be on a safe side? Or it is normal behavior for a library prepared with the nano kit?
Thanks in advance and have a great day!
I am trying to do adapter and low quality trimming of a fungal genome (prepared with Illumina DNA nano kit and sequenced with HiSeq 2000 100PE). After using BBduk to trim adapters and low quality reads as following
>./bbduk.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1_q25.fastq.gz out2=R2_q25.fastq.gz ktrim=r k=21 mink=11 hdist=2 tpe tbo ref=resources/adapters.fa qtrim=rl trimq=25
Still FASTQC showed a K-mer content warning for both R1 and R2 reads [ https://goo.gl/photos/Lsyt7YJeQnjB8HQq5 ]. Can I have your opinion how shall I handle my data? Shall I just remove the first 20 bases to be on a safe side? Or it is normal behavior for a library prepared with the nano kit?
Thanks in advance and have a great day!
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