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FASTQC report - kmer content and determining type of sequencing

Hello,

I have two questions:

1. Is there any way I can know what type of sequencing is used just by looking at FASTQC report? I have unknown file and just its FASTQC report: what I know is this:

Filename    C836.22Rv1.2.bam
File type   Conventional base calls
Encoding    Sanger / Illumina 1.9
Total Sequences 85988702
Sequence length 76

I also know the adapters used (Illumina Universal Adapter, Illumina Small RNA Adapter, Nextera Transposase sequence, SOLID Small Rna Adapter). Can I conclude by all of this that it was the RNA sequencing?

2. I had no overrepresented sequences and the adapter content is great, but I have this strange kmer content results. Can someone explain me this graph please?

enter image description here

fastqc
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updated by Ram Ram • written by tea.vuki • tea.vuki

Is there any way I can know what type of sequencing is used just by looking at FASTQC report

At best answer is a may be. RNAseq data generally have a characteristic nucleotide distribution (https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ ) but it is not a 100% guarantee of the experiment type.

You may find several blog posts about FastQC informative. Check them out: https://sequencing.qcfail.com/software/fastqc/

k-mer plots have been removed from new version of FastQC since they are not very informative. If you still have a plot then you are likely using an older version of FastQC.

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written by GenoMax GenoMax

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