search

epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
Other
60 stars 23 forks source link

taxonomy in the report #75

Closed HannahBenisty closed 9 months ago

HannahBenisty commented 11 months ago

Ask away!

Hi! I have done some samples and everything looks good in the report except for the taxonomy. I put you an example of a sample that has around 50% of cyanobacteria (in the sunburst and lineages). However, this is not displayed in the taxonomy when comparing with the other samples.

Pasted Graphic 5 Pasted Graphic 7 Pasted Graphic 6

nggvs commented 11 months ago

Hi @HannahBenisty , Thank you for your feedback, always welcome! The barplot shows the most abundant taxa taking into account all the samples. Are cianos abundant just in one sample or in many of them? You can sort the abundance table by the total and the most abundant phyla are the ones that should appear in the barplot.

HannahBenisty commented 11 months ago

Ahhh ok! thanks a lot for the clarification! cianos are predominant in two samples.

nggvs commented 11 months ago

However, I've seen them in the barplot, which are the samples that contains more cyanos?

HannahBenisty commented 11 months ago

True! in the legend, that is why I got confused. samples are the ones starting with LK3 or LK5. In the images is the example if LK5

nggvs commented 11 months ago

Would you mind to send me the two abundance tables? you can export it from the report (at the phyla level) and then there is another one in the output.