Hi
This is about the Illumina Hiseq based on Trueseq library.
Prior to trimming, the fastqc showed some k-mers enrichment in the middle and 5' end.
I performed the following
- quality trimming by seqtk,
- trimming based on adapters of trueseq3.fa in trimmomatic
Then I performed fastqc again.
The FastQC report shows that certain k-mers continue to be enriched.
I understand that I should remove the ones at the 5' end
But i m concerned about the k-mers at position 48-52. I have attached the plot. I would appreciate any suggestions whether i should ignore the k-mers or any further trimming would be necessary prior to further processing.
This is about the Illumina Hiseq based on Trueseq library.
Prior to trimming, the fastqc showed some k-mers enrichment in the middle and 5' end.
I performed the following
- quality trimming by seqtk,
- trimming based on adapters of trueseq3.fa in trimmomatic
Then I performed fastqc again.
The FastQC report shows that certain k-mers continue to be enriched.
I understand that I should remove the ones at the 5' end
But i m concerned about the k-mers at position 48-52. I have attached the plot. I would appreciate any suggestions whether i should ignore the k-mers or any further trimming would be necessary prior to further processing.
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