Awesome, thanks. That doesn't cover truncating sequences though, right?


On Tue, Jan 7, 2014 at 12:40 PM, Yoshiki Vázquez Baeza <
notifications@github.com> wrote:

> In ipynb/module2.ipynb:
>
> > +      "    'Format Template':'format_file.py -i %(template)s -k %(keys_for_replace)s -v %(values_for_replace)s -K %(keys_for_insert)s -V %(values_for_insert)s -o %(output)s',\n",
> > +      "    'To PDF':'module load texlive_2013; cd %(path)s; lualatex %(input)s',\n",
> > +      "    'To PNG':'inkscape -e %{png}s -d 300 %{pdf}s',\n",
> > +      "    'PDF Smash':'gs -r150 -q -sPAPERSIZE=ledger -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dFIXEDMEDIA -dPDFFitPage -dCompatibilityLevel=1.4 -sOutputFile=%(output)s -c 100000000 setvmthreshold -f %(pdfs)s'\n",
> > +      "    }"
> > +     ],
> > +     "language": "python",
> > +     "metadata": {},
> > +     "outputs": [],
> > +     "prompt_number": 21
> > +    },
> > +    {
> > +     "cell_type": "markdown",
> > +     "metadata": {},
> > +     "source": [
> > +      "Now, lets setup the paths and some helper methods. The first PCoA plot is a combination of the American Gut, Human Microbiome Project, Personal Genome Project and Global Gut datasets. These projects all used three different sequencing technologies however, and in order to combine them, we need to use the BIOM tables derived from sequence data all trimmed to the same length. See XXX for a more detailed discussion."
>
> It doesn't describe the challenges of the AG itself but it serves as a
> good reference:
>
> http://www.ncbi.nlm.nih.gov/pubmed/23861384
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/American-Gut/pull/53/files#r8703992>
> .
>