I am running fastQC on a Linux machine from the command line.
Until v.0.11.5, I was used to also get a kmer plot as an output.
Now, since v.0.11.6, Kmer output is disabled by default (see release notes) and I fail to find a way to enable it again.
I have tried running the program e.g. with the --kmers=7 option but neither in the .zip output, nor in the plot there is a kmer estimation.
Is it totally deprecated or did I miss something in the manual?
Thank you in advance.
Check https://github.com/s-andrews/FastQC/releases
RELEASE NOTES FOR FastQC v0.11.6
This update fixes some bugs and updates some of the functionality to accommodate changes in some of the sequencing platforms.
There is one major change which is that by default we now disable the kmer module. With the inclusion of the adapter plot the value of the information in the Kmer plot is often not great, and it is easy to confound it if there are any over-represented sequences, or primer compositional bias. Overall therefore we consider it best to not routinely include this module.
If you want to turn this module back on, then simply edit the limits.txt file in the Configuration folder of the FastQC installation and change the line near the top which says:
kmer ignore 1
..to..
kmer ignore 0
..and the module will be re-enabled.