fix idents

Author: antgonza

qiita_pet/support_files/doc/source/qiita-philosophy/index.rst

@@ -82,18 +82,22 @@ complex where a study with a defined set of collected samples can have subsets
 prepared in different ways so we can answer different questions. For example,
 let's imagine a study looking at how different `microbial communities changes
 during mammalian corpse decomposition
-<https://www.ncbi.nlm.nih.gov/pubmed/26657285>`__.; thus, your full study design
+<https://www.ncbi.nlm.nih.gov/pubmed/26657285>`__; thus, your full study design
 is to collect a set of samples, which you will then process with 16S, 18S and
 ITS primers. This will result in 1 sample and 3 preparation information files,
 `see it in Qiita <https://qiita.ucsd.edu/study/description/10141>`__.
 
-Now, let's imagine other more complex examples:
+Now, let's imagine other more complex example:
+
 1. All of the samples were prepped for 16S and sequenced in two separate
-  MiSeq runs
-2. 50 of the samples were prepped for 18S and ITS, and sequenced ina single
-  MiSeq run
+   MiSeq runs
+
+2. 50 of the samples were prepped for 18S and ITS, and sequenced in a single
+   MiSeq run
+
 3. 50 of the samples were prepped for WGS and sequenced on a single
-  HiSeq run
+   HiSeq run
+
 4. 30 of the samples have metabolomic profiles
 
 To represent this project in Qiita, you will need to create a single
@@ -105,36 +109,36 @@ file. For instance, the data sets described above would require the following
 data and prep information:
 
 1. All of the samples prepped for 16S and sequenced in two separate
-  MiSeq runs
+   MiSeq runs
 
-  a) 1 prep information file describing the two MiSeq runs (use a
-     run\_prefix column to differentiate between the two MiSeq runs, more
-     on metadata below) where the 100 samples are represented
-  b) the 4-6 fastq raw data files without demultiplexing (i.e., the
-     forward, reverse (optional), and barcodes for each run)
+   a) 1 prep information file describing the two MiSeq runs (use a
+      run\_prefix column to differentiate between the two MiSeq runs, more
+      on metadata below) where the 100 samples are represented
+   b) the 4-6 fastq raw data files without demultiplexing (i.e., the
+      forward, reverse (optional), and barcodes for each run)
 
 2. 50 of the samples prepped for 18S and ITS, and sequenced in a single
-  MiSeq run
+   MiSeq run
 
-  a) prep information files, one describing the 18S and the other describing the
-     ITS preparations
-  b) the 2-3 fastq raw data files (forward, reverse (optional), and
-     barcodes)
+   a) prep information files, one describing the 18S and the other describing the
+      ITS preparations
+   b) the 2-3 fastq raw data files (forward, reverse (optional), and
+      barcodes)
 
 3. 50 of the samples prepped for WGS and sequenced on a single HiSeq run
 
-  a) 1 prep information files describing how the samples were multiplexed
-  b) the 2-3 fastq raw data files (forward, reverse (optional), and
-     barcodes).
-  c) NOTE: We currently do not have a processing pipeline for WGS but
-     should soon.
+   a) 1 prep information files describing how the samples were multiplexed
+   b) the 2-3 fastq raw data files (forward, reverse (optional), and
+      barcodes).
+   c) NOTE: We currently do not have a processing pipeline for WGS but
+      should soon.
 
 4. 30 of the samples with metabolomic profiles
 
-  a) 1 prep information file. the raw data file(s) from the metabolomic
-     characterization.
-  b) NOTE: We currently do not have a processing pipeline for metabolomics but
-     should soon.
+   a) 1 prep information file. the raw data file(s) from the metabolomic
+      characterization.
+   b) NOTE: We currently do not have a processing pipeline for metabolomics but
+      should soon.
 
 Portals
 -------