Question: Problem when using Fastqc overrepresented sequences to find adapter
0
gravatar for Sean Liang
3.0 years ago by
Sean Liang0
Sean Liang0 wrote:

Hi all:

I am totally new to NGS data analysis. Recently I am analyzing the small RNA sequencing data from Illumina devices, in the first trim process, I used fastqc to look into the raw data for adapter seeking, and got the overrespresented sequences result as indicated in below picture. I am totally confused about this result and have no idea which sequence is the adapter. Could you please have a look at it for me?

result

rna-seq next-gen • 1.1k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Sean Liang0

There is a Button Adapter Content, you should check that.

ADD REPLYlink written 3.0 years ago by Michael Dondrup46k

Thanks Micheal, I checked the adaptor content and got this information, does this mean the adaptors have already been trimmed?

result

ADD REPLYlink written 3.0 years ago by Sean Liang0

This looks good to me. Also, there should not be a standard single end adapter in a small RNA sample. Normally I tend to ignore the overrepresented sequences tab.

ADD REPLYlink written 3.0 years ago by Michael Dondrup46k

Thanks a lot for your help Micheal.

ADD REPLYlink written 3.0 years ago by Sean Liang0
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