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Old 04-21-2017, 06:39 AM   #1
Vinn
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Default K-mer content failed on 5' end - advice needed

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!

Last edited by Vinn; 04-21-2017 at 06:47 AM.
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Old 04-21-2017, 07:14 AM   #2
GenoMax
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What kind of analysis are you trying to do? In general I have never worried about k-mer warnings from FastQC.
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Old 04-21-2017, 07:17 AM   #3
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Quote:
Originally Posted by GenoMax View Post
What kind of analysis are you trying to do? In general I have never worried about k-mer warnings from FastQC.
Hi GenoMax, thanks for your reply. I would like to do de novo assembly.
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Old 04-21-2017, 07:43 AM   #4
GenoMax
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Take a look at @Brian's suggestions in this thread. I have provided a link for a specific post but take a look at the whole thread. He should be along with more later.
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Old 04-21-2017, 07:48 AM   #5
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Thank you, I will read the thread through.
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fastqc, genome assembly, illumina, quality control

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