fastqc gc-content peak and adapter content

Question

[David]

Hi,

I have the following fastqc profile and i´m just trying to understand what´s wrong with blue line. This is a human microRNA rna seq experiment (1x50bp) from human blood extracted microRNAs.

In adapter content it starts around 18 (y axis) (small RNA 3´adapter). Why is that ?? Too much adapter ??

In the GC content i have a pick at 50%. Is that primer dimer or any type of contamination??

Thanks !!!!

Answer 1

[GenoMax]

In adapter content it starts around 18 (y axis) (small RNA 3´adapter). Why is that ?? Too much adapter ??

Small RNA are supposed to be just that .. small. Since you are sequencing 50 cycles it is normal to expect seeing adapters in your sequence. In this case that result seems to be fine. Go ahead and start your analysis. One of the first steps will be trimming off this adapter sequence in preparation for downstream alignments.

[David]

Ok great. Yes I will start cleaning data. thanks