Question: fastqc gc-content peak and adapter content
0
gravatar for David
2.0 years ago by
David150
David150 wrote:

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 ??

enter image description here

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

[1]: http://i.imgur.com/kgckobJ.png

Thanks !!!!

fastqc • 1.7k views
ADD COMMENTlink written 2.0 years ago by David150
2
gravatar for genomax
2.0 years ago by
genomax68k
United States
genomax68k wrote:

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.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by genomax68k

Ok great. Yes I will start cleaning data. thanks

ADD REPLYlink written 2.0 years ago by David150
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