Weird cladogram


I have filtered table and sequences using qiime2 instruction (frequency-based & mitochondria, chloroplast, Archaea, Eukaryota). However, the dimension of table did not change after using filter and the number of taxa was 854 before and after using filters. Also, the output cladogram shows lots of taxonomy which is not different based on our target variable. Please see the below cladogram. I was wondering if you could please let me know if I miss any step.


Can you post the command you used to build that cladogram?


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Thanks for your reply. I included "filtering commands" and "commands to make biom file to use in Galaxy website". Thanks!

Filtering commands:

qiime feature-table filter-features --i-table filtered-table-dada.qza --p-min-frequency 2 --o-filtered-table filtered-feature-table-dada.qza

qiime taxa filter-table --i-table filtered-feature-table-dada.qza --i-taxonomy taxonomy.qza --p-include p__ --p-exclude mitochondria,chloroplast --o-filtered-table filtered-no-mitochon.qza

qiime taxa filter-table --i-table filtered-no-mitochon.qza --i-taxonomy taxonomy.qza --p-exclude "k__Archaea" --o-filtered-table filtered-no-mitochon-archaea.qza 

qiime taxa filter-table --i-table filtered-no-mitochon-archaea.qza --i-taxonomy taxonomy.qza --p-exclude "k__Eukaryota" --o-filtered-table filtered-no-mitochon-archaea-eukarya.qza

qiime taxa filter-seqs --i-sequences Seq-trim-dada2_240-140_T1.qza --i-taxonomy taxonomy.qza --p-include p__ --p-exclude mitochondria,chloroplast --o-filtered-sequences filtered-seq-no-mito.qza

qiime taxa filter-seqs --i-sequences filtered-seq-no-mito.qza --i-taxonomy taxonomy.qza --p-exclude "k__Archaea" --o-filtered-sequences filtered-seq-no-mito-archea.qza

qiime taxa filter-seqs --i-sequences filtered-seq-no-mito-archea.qza --i-taxonomy taxonomy.qza --p-exclude "k__Eukaryota" --o-filtered-sequences filtered-seq-no-mito-archea-euka.qza

Making biom file to use in Galaxy:

qiime taxa collapse --i-table filtered-no-mitochon-archaea-eukarya.qza --o-collapsed-table collapse-filtered-table.qza --p-level 6 --i-taxonomy taxonomy.qza

qiime feature-table relative-frequency --i-table collapse-filtered-table.qza --o-relative-frequency-table collapse-frequency-table.qza --output-dir collapse.freq/

qiime tools export --input-path collapse-frequency-table.qza --output-path collapse.freq

biom convert -i collapse.freq/feature-table.biom -o collapse.freq/collapse.table.txt --header-key "taxonomy" --to-tsv
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This looks fine to me. I have no idea why that would happen :thinking:

Does anyone else have an idea?

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Thanks for your reply. Also, I have pasted the commands for quality control (dada2) as well as classifier to assign taxonomy based on SILVA database for any clue. Thanks!

Command for quality control (dada2)
qiime dada2 denoise-paired --i-demultiplexed-seqs Sequences.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 240 --p-trunc-len-r 220 --o-representative-sequences Seq-trim-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza

Command for assign taxonomy based on SILVA database
qiime feature-classifier classify-sklearn
--i-classifier ../silva138_AB_V4_classifier.qza
--i-reads Seq-trim-dada2_240-140_T1.qza
--o-classification taxonomy.qza

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Hi @Barandouzi,

This looks like LEfSe output. If it is, then this is not a true cladogram, despite name of the function. It is merely a dendrogram based on taxonomic ranks, were each node is a taxonomic level. If you do not have | separating the ranks, then you're only ever going to see this "star" cladogram. Where each tip is a unique full taxonomy string.

I'd recommend installing dokdo into your QIIME 2 environment and then run the prepare-lefse command. Then upload to LEfSe Galaxy.


Thanks! It solved the issue.

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