What file can i use

Equiroz · June 29, 2020, 6:14pm

Hello everyone

I want to work an analysis with picrust 2, at the moment of entering my .biom files, it asks me for the table of DNA_sequences.fasta, that table in which file of which mothur generates during the analysis of 16s can I find it and under what name, I believed it could be: stability.trim.contigs or stability.trim.contigs.good.

Kind regards

pschloss · June 30, 2020, 5:51pm

I’m not a big fan of the picrusts, but you can see how we ran it with mothur-generated files using the code in this script…

github.com

SchlossLab/Sze_SCFACRC_mBio_2019/blob/2446a0e73282d69f3f798e59006833ada33c6fbc/code/picrust2.sh

THREADS=6

module load python-anaconda3/latest
module load R/3.5.1

WORKDIR=data/picrust2
rm -rf $WORKDIR
mkdir -p $WORKDIR

#dependencies
FASTA=$WORKDIR/crc.asv.fasta
BIOM=$WORKDIR/crc.asv.biom

R -e "source('code/picrust2_utilities.R'); sort_and_unalign_sequences()"

mothur "#make.biom(shared=data/asv/crc.asv.shared, outputdir=$WORKDIR)"

mv $WORKDIR/crc.asv.ASV.biom $BIOM

conda activate

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system · July 10, 2020, 5:51pm

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What file can i use

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