addressing @ackermag and @ElDeveloper comments

Author: antgonza

README.rst

@@ -52,7 +52,7 @@ Accepted raw files
 * Multiplexed SFF
 * Multiplexed FASTQ: forward, reverse (optional), and barcodes
 * Per sample FASTQ: forward
-* Multiplexed fasta/qual files.
+* Multiplexed FASTA/qual files
 
 Known issues
 ------------

qiita_pet/support_files/doc/source/_static/my-styles.css

@@ -1,3 +1,7 @@
 .navbar-brand > img {
     display: inline-block;
   }
+
+.red {
+    color:red;
+}

qiita_pet/support_files/doc/source/faq.rst

@@ -6,15 +6,14 @@ What kind of data can I upload to Qiita for processing?
 
 Processing in Qiita requires 3 things: raw data, sample and prep information
 files. `Here <https://github.com/biocore/qiita/blob/master/README.rst#accepted-raw-files>__`
-a list of currently supported raw files files. Note that we are accepting
-any kind of target gene (16S, 18S, ITS, whatever) as long as there is
-some kind of demultiplexing strategy. You can also upload WGS however, WGS
-processing is not ready.
+you can find a list of currently supported raw files files. Note that we are
+accepting any kind of target gene (16S, 18S, ITS, whatever). You can also upload
+WGS however, WGS processing is not ready.
 
 What's the difference between a sample and a prep information file?
 -------------------------------------------------------------------
 
-Sample information file is the information about the samples, including
+A sample information file describes the samples in a study, including
 environmental factors relating to the associated host. The prep information
 file has information on how the sample was processed in the wet lab. If you
 collected 100 samples for your study, you will need 100 rows in your sample
@@ -32,33 +31,35 @@ Example study processing workflow
 
 A few more instructions: for the example above the workflow should be:
 
-#. Create a new study
-#. Add a sample information file, you can add 1, try to process it and the
+#. **Create a new study.**
+#. **Add a sample information file.** You can add 1, try to process it and the
    system will let you know if you have errors or missing columns. The
    most common errors are: the sample name column should be named
    sample\_name, duplicated sample names are not permitted. For a full list of
    required fields, visit :doc:`tutorials/prepare-information-files`.
-#. Add a prep information file to your study for each data type. The prep
+#. **Add a prep information file to your study for each data type.** The prep
    information file should contain all the samples in the sample information
    file or a subset. If you have more than one FASTQ file set (forward,
-   reverse (optional) and barcodes) you will need to add a run_prefix
-   column. A prep information file and a QIIME compatible mapping file will
+   reverse (optional) and barcodes) you will need to add a
+   :ref:`run_prefix <required-fields-for-preprocessing-target-gene-data>`
+   column.
+   A prep information file and a QIIME compatible mapping file will
    be available for download after the prep information file is added
    successfully.
-#. Upload and link your raw data to each of your prep information files.
+#. **Upload and link your raw data to each of your prep information files.**
    Depending on your barcoding/sequencing strategy you might need 1 or more
-   raw datas file sets. If you have 2 raw data sets you may have to rename one
+   raw data file sets. If you have 2 raw data sets you may have to rename one
    set so that each set has a different name. If they have the same name they
    will over-write on upload. Note that you can have one FASTQ file set linked
    to more than one prep information file.
-#. Preprocess your files. For target gene amplicon sequencing, this will demux
+#. **Preprocess your files.** For target gene amplicon sequencing, this will demux
    and QC. There are multiple options for preprocessing depending on the
    barcode format and the data output from the sequencing center - this may
    require a series of trial and error to establish the correct option for
    your data files. After demultiplexing a log file is generated with
    statistics about the files demultiplexed including the number of sequences
    assigned per sample.
-#. Process each of your preprocessed data types. For target gene, this will
-   perform close OTU picking against the latest version of Greengenes and can
+#. **Process each of your preprocessed data types.** For target gene, this will
+   perform closed OTU picking against the latest version of Greengenes and can
    be quite time consuming depending on the number of samples and the depth
    of sequencing.

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

@@ -13,7 +13,7 @@ environments for each pipeline gives the freedom of adding any pipeline with
 any software dependencies to Qiita. Artifacts, basically any file in the
 system, from raw sequence to contingency tables or even data visualizations,
 permits the system to store any kind of data but also define within each
-pipelines which commands and parameter can applied to them.
+pipelines which commands and parameters can applied to them.
 
 The current plugins available are:
 

qiita_pet/support_files/doc/source/tutorials/ebi-submission.rst

@@ -2,6 +2,8 @@
 
 .. index:: ebi-submission
 
+.. role:: red
+
 EBI submission via Qiita
 ========================
 
@@ -19,10 +21,11 @@ help send an email to `qiita.help@gmail.com <qiita.help@gmail.com>`__. Help will
 advice on additional fields to add to ensure MiXs compliance.
 
 Note that submissions are time consuming and need full collaboration from the user.
-Do not wait until the last minute to request help. In general, the best time to request a submission
-is when you are writing your paper. Remember that the data can be submitted to EBI and can be
-kept private and simply make public when the paper is accepted. Note that EBI/ENA takes up to 15 days to
-change the status from private to public, so consider this when submitting data and your manuscript.
+:red:`Do not wait until the last minute to request help.` In general, the best
+time to request a submission is when you are writing your paper. Remember that the
+data can be submitted to EBI and can be kept private and simply make public when
+the paper is accepted. Note that EBI/ENA takes up to 15 days to change the status
+from private to public, so consider this when submitting data and your manuscript.
 
 .. note::
    For convenience Qiita allows you to upload a QIIME mapping file to process your data. However,

qiita_pet/support_files/doc/source/tutorials/no-raw-sequences.rst

@@ -57,7 +57,7 @@ named ``forward`` and all of our reverse reads are in a folder named
     cat forward/*.fastq > forward.fastq
     cat reverse/*.fastq > reverse.fastq
 
-While there is no requirement to comprass the generated files, it makes data
+While there is no requirement to compress the generated files, it makes data
 transfer and storage more convenient. The preferred and only supported
 compression program to use is ``gzip``:
 

qiita_pet/support_files/doc/source/tutorials/prepare-information-files.rst

@@ -64,7 +64,7 @@ the centralized `Qiita server <http://qiita.microbio.me>`__:
 +-----------------------------------+----------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``physical_specimen_remaining``   | ``TRUE`` or ``FALSE``                                                | Is there still physical sample (e.g., soil, not DNA) available?                                                                                                                                                                                                                                                                                   |
 +-----------------------------------+----------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``dna_extracted``                 | ``y`` or ``n``                                                       | Has DNA already been extracted for this sample?                                                                                                                                                                                                                                                                                                   |
+| ``dna_extracted``                 | ``TRUE`` or ``FALSE``                                                | Has DNA already been extracted for this sample?                                                                                                                                                                                                                                                                                                   |
 +-----------------------------------+----------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``latitude``                      | `decimal degrees <http://en.wikipedia.org/wiki/Decimal_degrees>`__   | Latitude where sample was collected.                                                                                                                                                                                                                                                                                                              |
 +-----------------------------------+----------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -108,7 +108,7 @@ system:
 Required fields for EBI submission
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-These are the columns required for successfully submit your data to EBI:
+Without this columns you will not be able to submit to EBI. These are the columns required for successfully submit your data to EBI:
 
 +-------------------------------------+-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Field name                          | Format                                    | Description                                                                                                                                                                                                    |
@@ -117,7 +117,7 @@ These are the columns required for successfully submit your data to EBI:
 +-------------------------------------+-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``center_name``                     | free text                                 | Name of the sequencing facility.                                                                                                                                                                               |
 +-------------------------------------+-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``platform``                        | ``Illumina`` or ``LS454``                 | The sequencing technology used in the study. ``Illumina`` sequencing data was generated on an Illumina platform; ``LS454`` sequencing data was generated on a 454 pyrosequencing.                              |
+| ``platform``                        | ``Illumina`` or ``LS454``                 | The sequencing technology used in the study. ``Illumina`` sequencing data was generated on an Illumina platform; ``LS454`` sequencing data was generated on a 454 pyrosequencing platform.                     |
 +-------------------------------------+-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``instrument_model``                | see table below                           | The sequencing instrument model used for sequencing. See table below for valid options.                                                                                                                        |
 +-------------------------------------+-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -136,6 +136,8 @@ Valid values for instrument_model per platform, taken from ftp://ftp.sra.ebi.ac.
 | ``Illumina`` | ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, ``Illumina Genome Analyzer Ix``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 2000``, ``Illumina HiSeq 1500``, ``Illumina HiSeq 1000``, ``Illumina MiSeq``, ``Illumina HiScanSQ``, ``HiSeq X Ten``, ``NextSeq 500``, ``unspecified`` |
 +--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
+.. _required-fields-for-preprocessing-target-gene-data:
+
 Required fields for pre-processing target gene data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~