Fastqc, Trimming And Kmers

Question

[int11ap1]

Good morning everybody,

I had RNA-seq data from Illumina (paired-ends), which adapters were removed and quality trimming performed successfully using Trimmomatic. After analysing with FastQC, all seems OK. However, there are one thing that worries me: the kmers. Some pictures:

Why is it? Apparently, there are no overrepresented sequences according to FastQC.

[Daniel]

Just to note, the images aren't showing up for me in either Chrome of Firefox

Answer 1

[jackuser1979]

Have you checked FastQC website?. These examples will give you an idea whats wrong with your sequence:

Overrepresented Kmers: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/11%20Overrepresented%20Kmers.html

Sequence Length Distribution: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/8%20Sequence%20Length%20Distribution.html

[Adrian Pelin]

That site tells you what is happening and how, but doesn't tell you why or potential scenarios.