k-mers in the middle of the read

[A-K]

Hi All,

I'm new to RNASeq analysis and am looking for some advice on the FastQC k-mer output.

For several of my samples, I see accumulation of k-mers in the middle of the read. (see attached).

Does anyone have experience with this / know what the cause could be?

Your help is much appreciated,

A-K

[asier_gonzalez]

Hey there,

If I'm not wrong, this probably means that there were many fragments that were shorter than 40-50 bp, that is, those overepresented sequences are probably the adaptors.

Let's see what more experienced people think.

Regards,

Asier

[HESmith]

The over-represented sequence (CTCGTATGCCGT) is from the TruSeq index adapter (the segment immediately following the index). The spacing is consistent with adapter dimers. It appears that the data were trimmed, which removed the adapter sequences preceding the index but not those that followed.

[A-K]

Thanks both for the quick replies! Very helpful!