Tried to do the corrections but i'm really at a loss on the whole github
thing.
when you or adam will be in, if you can explain to me the idea how it works
i'll insert the changes.



On Mon, Dec 30, 2013 at 10:17 AM, 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 progress on this Amnon? We *really* need to get this finished.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/50/files#r8587790>
> .
>