Any word from Amnon on this?


On Mon, Dec 16, 2013 at 5:51 PM, adamrp <notifications@github.com> wrote:

> In ipynb/contaminant_filtering.ipynb:
>
> > +     "collapsed": false,
> > +     "input": [
> > +      "!filter_fasta.py -f $merged_sequences_fp -o $merged_sequences_fecal_only_fp --mapping_fp=$merged_mapping_file_fp --valid_states=\"BODY_SITE:UBERON:feces\""
> > +     ],
> > +     "language": "python",
> > +     "metadata": {},
> > +     "outputs": []
> > +    },
> > +    {
> > +     "cell_type": "markdown",
> > +     "metadata": {},
> > +     "source": [
> > +      "The filtering will proceed according to the following steps:\n",
> > +      "\n",
> > +      "1. Identify the most abundant Gammaproteobactia and select the representative sequences from the most abundant, such that the cumulative abundance of remaining Gammaproteobacteria is no greater than 3%\n",
> > +      "2. Find all sequences in the American Gut sequences that map to these OTUs at 97PI\n",
>
> I'll change it once Amnon has the opportunity to see the rest of these
> comments.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/50/files#r8389025>
> .
>