Question: Reads with failing Kmer enrichment in FastQC - priming bias?
0
gravatar for Ismaelrymy
10 days ago by
Ismaelrymy0
Ismaelrymy0 wrote:

Hi there!

I am performing a quality check in a transcriptomic dataset before attempting a de-novo assembly. Duplication is high, as expected, but I did not expect this results in the k-mer graph:

enter image description here

No sequence is overrepresented in FastQC, whereas this makes me think that reads starting with "CCGACTTTGGACGAG" are overrepresented. Trimming, while giving very good results in other aspects, does not solve this problem, these are the results (sliding window; 15 bp headcrop; minmmum length applied).

enter image description here

What do you think that may be causing this? How would you continue?

Thank you in advance.

rna-seq fastqc kmer quality • 42 views
ADD COMMENTlink modified 10 days ago by Jennifer Hillman Jackson25k • written 10 days ago by Ismaelrymy0
1
gravatar for Jennifer Hillman Jackson
10 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

This is expected when the library preparation uses random primers. If that is true for your case (seems so), the warning can be ignored.

Help: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/11%20Kmer%20Content.html

Thanks, Jen, Galaxy team

ADD COMMENTlink written 10 days ago by Jennifer Hillman Jackson25k
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