Some contradiction in fastqc

Question

[zizigolu]

Hey guys,

In GSE67387 data data sets, in FastQC result panels, over-represented sequences are different among samples and there is no hit in adapter content, then from where I should access the adapter sequence please? The author did not respond to my email. Do you have any suggestions?

Answer 1

[Biomonika (Noolean)]

FastQC was never meant to detect adaptors, it detects over-represented sequences which makes it sometimes detect untrimmed adaptors. Maybe your data have very low proportion of adaptors and you are discovering true biological sequence at high abundance. Try blasting those sequences to find out what they are.

[zizigolu]

Sorry, then which sequence should I use in cutadapt as adapter because as I told the author did not reply to my email?

[Biomonika (Noolean)]

Maybe take a look at my blog (http://sites.psu.edu/biomonika/2015/07/03/trim-now-or-never-pe-and-mp-adaptor-removal/). In any case, you need to provide more information about your data - which technology (Illumina?) which machine (MiSeq? Hiseq?). Not everyone is familiar with GSE67387. Also, your question now is how to detect adaptors in the data which there are plenty good answers on biostars already, try searching for them.

[zizigolu]

Thank you very much