Remove chloroplast and mitochondria from philogenetic tree

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Deb Colman

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Apr 17, 2020, 3:56:31 PM4/17/20
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Hi Qiimers!! I removed chloroplast and mitochondria otus from otu_table.biom and at the same time I would want to eliminate these otus from the philogenetic tree...I ran:

filter_tree.py -i rep_seqs.tre -t tips_to_keep.txt -o negated.tre -n

Is this the command right? Is there other way to eliminate these sequences from the tree?


I attach you ´tips to keep.txt'


Thanks!
tip_tree_Chlorop_Mitoch

TonyWalters

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Apr 17, 2020, 4:16:00 PM4/17/20
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Hello Deb,

Usual disclaimer that qiime1 is no longer being updated, and qiime2 will be preferable for new options/support in the future.

You might want to go back to the rep_set.fna sequence, filter the mitochondria and chloroplast there (http://qiime.org/scripts/filter_fasta.html and pass your filtered OTU table as -b input), and then on the resulting filtered fasta file, do alignment, alignment filtering, and tree building. This would be so any alteration to filtering (the base positions that were highly gapped, for example) would reflect an alignment without the plastic/mitochondria sequences. However, it might not change the tree-apart from getting rid of the unwanted tips.

But if you wanted to filter at the tree level itself, you have to pass a tab-delimited text file with the OTU IDs as the first column, rather than the taxonomy strings.
You could convert your (already filtered) biom OTU table to tab delimited form, with this example command:
biom convert -i table.biom -o table.from_biom.txt --to-tsv

You might have to remove the first lines with # in front of them, so it's just the OTU IDs remaining, then pass as the tab-delimited table as the -t parameter for filter_tree.py (don't use -n).
-Tony

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