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kmer content failling with fastqc
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13 months ago
France

Dear all I have trimmed my data(illumina 2*150PE) using bbduk from bbmap suite and still have this issue with fastqc (see photos) as failling kmer content, do you have any suggestion to deal with this problem befor downstream analysis? thank you very much. kmercontent enter image description here

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I suggest that you not worry about the kmer content failing and move forward with the analysis. This has been one of the tests that is now turned off by default in new FastQC since it causes new people to worry for not always valid reasons.

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Indeed. I have never once seen any sample that has passed all of these FASTQC parameters.

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In my experience kmer content often seems to fail, and I've never figured out why. Nor has it ever seemed to really matter for downstream assembly etc.

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You did not link a picture, and might read this first.

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Please follow these steps to upload pictures How to add images to a Biostars post

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kmer summary_PNG

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did you compare them against the index sequences?

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No, how can I proceed ?

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Whilst 5' seems trimmed it looks like 3' is not. Did you trimmed both ends ?

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thank you all for your answer.

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If you already trimmed both ends you may have to start the trimming over again changing your adapter sequence file. Find your entire repeated sequence in your original reads then do the trimming again with the modified file.

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