Question: why FastQC tool K-mer content parameter is absent?
0
gravatar for esraesmeray1990
8 weeks ago by
esraesmeray199010 wrote:

Hi I used fastqc tool after running Afterqc tool but at the result I saw k-mer content parameter is absent. what could be the reason of it and how should i add k-mer content to analysis?

by the way, I run FastQC after Fastp tool for the same data and there was k-mer content.

afterqc wts fastp fastqc k-mer • 109 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by esraesmeray199010
1

Which version of FastQC did you use ? AFAIK libraries barely never pass the k-mer content test and was not a mark of data quality. So maybe they removed the fonctionnality

Edit : Here, check the FastQC changelog : https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

21-12-17: Version 0.11.6 released

Disabled the Kmer plot by default

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Bastien HervĂ©3.7k

I used Version 0.11.8.

ADD REPLYlink written 8 weeks ago by esraesmeray199010

So, by default it's disabled (since 0.11.6). Look at the FastQC options the enable it

ADD REPLYlink written 8 weeks ago by Bastien Hervé3.7k

It seems easy but if you don't know the reason it would be a big problem, the problem is solved thank you a lot.

ADD REPLYlink written 8 weeks ago by esraesmeray199010
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