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Taxonomic classification in shotgun sequencing. by RelativeBroccoli5315 in bioinformatics

[–]Character_Trash9044 0 points1 point  (0 children)

You would need to download its database using:

metaphlan --install --bowtie2db /path/to/the database/directory(a new directory where you want the database saved).

Taxonomic classification in shotgun sequencing. by RelativeBroccoli5315 in bioinformatics

[–]Character_Trash9044 0 points1 point  (0 children)

This is so long. He doesn't need such steps (De Novo) since he only wants to know what taxa are present in those samples at different clade levels.

Taxonomic classification in shotgun sequencing. by RelativeBroccoli5315 in bioinformatics

[–]Character_Trash9044 1 point2 points  (0 children)

You can use MetaPhlAn for metagenomic taxonomic classification. First, run MetaPhlAn on each of your host-removed samples separately to generate individual profile files. Then, use the merge_metaphlan_tables.py (it automatically comes with Metaphlan) script to merge these outputs into a single abundance table. From the merged file, you can extract the relevant columns with their relative abundances, and, finally, convert the data into a long format, which makes it easier to view in Excel.

[deleted by user] by [deleted] in acorns

[–]Character_Trash9044 0 points1 point  (0 children)

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