Nothing yet; @amnona?

Adam


On Sun, Dec 22, 2013 at 6:39 PM, Daniel McDonald
<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",
>
> Any word from Amnon on this?
> … <#1431d1b732c72155_>
> 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> .
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/50/files#r8521874>
> .
>