Are truseq adapter sequences picked up by FASTQC?

Question

[bioinfo]

Hello,

I am testing a new software that is supposed to automatically detect adapters and remove them. I am using the adapters shown here: https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/TruSeq/UDIndexes.htm

I run the demultiplexing+ adapter trimming and the software does not see to recognize this adapter. However, when I check the data with fastqc I notice that it does not seem to find adapters on the adapter content plot. Does anyone know if fastqc can detect the adapters from the link above? I have not been able to find which adapters fastqc can detect.

Thank you

Answer 1

[GenoMax]

FastQC checks for the core adapter sequence that is present at beginning of adapter sequences. They are contained in this file: https://github.com/golharam/FastQC/blob/master/Configuration/adapter_list.txt

You can edit the file and add sequence you want to detect. truseq adapters have a common initial sequence that is included in the link you have in your post.

[bioinfo]

Thank you so much! I see that the sequence for the Illumina Universal Adapter on fastqc is AGATCGGAAGAG. The ones from the Illumina website start with this sequence but contain extra bases. That means that fastqc would pick up both of them right?

[GenoMax]

Yes it should. It may use the "identifier" that is in the adapters config file. So it may call the results "Illumina universal adapter" instead of "TruSeq".