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biomtotxt.sh

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alk224 edited this page Jun 4, 2015 · 4 revisions

Convert a biom-formatted OTU table to tab-delimited.

Usage:

biomtotxt.sh (InputBiomTable)

This script takes an OTU table produced in QIIME (biom format) and returns the same table in tab-delimited format (.txt). It assumes you are using the version of biom found in a typical QIIME install on a Linux system. It will retain the metadata field "taxonomy."

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AKUTILS WIKI HOME
Data processing tutorial

Script pages:
akutils_command_list.sh
akutils_config_utility.sh akutils_dependency_check.sh align_and_tree_workflow.sh
biom-summarize_folder.sh biomtotxt.sh cdiv_graphs_and_stats_workflow.sh
concatenate_fastqs.sh
db_format.sh Dual_indexed_fqjoin_workflow.sh
ITSx_parallel.sh
mapcats.sh otu_picking_workflow.sh PhiX_filtering_workflow.sh
Single_indexed_fqjoin_workflow.sh
strip_primers.sh
txtttobiom.sh

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