mothur

Mothur file to biom

#1

Hi,

Somebody could guide me in the transformation of some files generate in mothur to biom format. This is because I want to use PICRUST, I found an example in https://t.co/1BvNMUlNRU but i dont understand which shared file need. Best regards

#2

Here’s what we’ve done…

mothur "#list.otus(shared=crc.shared);get.otus(constaxonomy=crc.cons.taxonomy, accnos=crc.0.03.otulabels);make.biom(shared=current, constaxonomy=current, label=0.03, reftaxonomy=gg_13_5_99.gg.tax, picrust=97_otu_map.txt)"

# Comments on whether this is an acceptable biom format
biom validate-table -i crc.0.03.biom

# Convert to an acceptable biom format for picrust
biom convert --table-type="OTU table" -i crc.0.03.biom -o temp_OTU_table.txt --to-tsv --header-key taxonomy
biom convert -i temp_OTU_table.txt -o $BIOM --table-type="OTU table" --to-json --process-obs-metadata taxonomy

# Double check that it is now the right format
biom validate-table -i crc.0.03.biom

# Run the picrust v1 program to make predictions
normalize_by_copy_number.py -i crc.0.03.biom -o crc.normalized.biom
predict_metagenomes.py -f -i crc.normalized.biom -o crc.metagenomes.tsv -a crc.nsti

In this workflow, everything is run from the command line. crc.shared was generated by running make.shared on the output of cluster/cluster.split, which generated 0.03 OTUs. The crc.cons.taxonomy file was generated by running classify.otu.

Hope this helps a bit,
Pat

#3

Thanks a lot for your helpful reply Pat