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HI <@UE4L64T4G> I installed latest version of mult...
# multiqc
i
HI @Phil Ewels I installed latest version of multiqc (1.32) and I noticed that I don't have bracken section in my multiqc report anymore. Is bracken still supported in multiqc? I cannot also find it in Supported Tools of multiqc.
e
Must have been removed since v1.25.1, as being part of Kraken: https://github.com/MultiQC/MultiQC/releases/tag/v1.25.1
p
So the section should still be there, just named Kraken instead. Is that the case @Ivan Baksic?
i
Hi Evangelos, hi Phil, Thank you for your quick responses! As far as I understand, multiqc now takes data from bracken and puts it into kraken section. However, This way I lose the information about the unclassified number of reads reported by kraken. This is quite valuable to qc report because it means that the reference used does not contain the organism that is a part of the sample.
Example: multiqc 1.32:
multiqc 1.21:
p
Hmm, that looks a bit buggy.. In fact your 1.21 screenshot data is already showing up as Kraken (that's why we merged the two)
It looks a bit like the Braken output is overriding / replacing the Kraken output that was there previously
Could you open a GitHub issue with the Braken output data used for those screenshots please?
MultiQC dev is going slowly at the moment as it's just me, but I'll get to it ASAP
i
All good! no rush from my side. I can always revert to older version. I will make a github issue. Thank you for your support!
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I created the issue here: https://github.com/MultiQC/MultiQC/issues/3393 Please let me know if I forgot something and should add it. Thank you once again!
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p
Thanks! You attached the FastQ files, but could you attach the kraken outputs instead please? Saves me having to mess around running Kraken and trying to reproduce that part myself.
It should be in the Nextflow work directory for the run, if in doubt
i
Thanks! I added them!
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