Format genus table for LEfSe

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1

Hello,

When I create my taxa collapsed genus table I get a lot of blanks at the genus level, which I understand is not unusual. For example:

k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Leuconostocaceae|g__Leuconostoc
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Leuconostocaceae|g__

However, when I use this table to create LEfSe plots the blanks still show up. Is there a way to add “unclassified” to blank genus assignment in QIIME2? I am using QIIME2018.8 on a cluster, which is the only version available on the cluster.

Thanks!

2

Hello@Akriti,
I would adopt the method ALDEx2 or ANCOM2 for such analysis instead of LEfSe, because of the obvious issues that have been clearly laid down in recent publications, for e.g., Fernandes, A.D., Reid, J.N., Macklaim, J.M., McMurrough, T.A., Edgell, D.R., and Gloor, G.B. (2014). Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome 2, 15-15. doi: 10.1186/2049-2618-2-15.

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