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8 changes: 4 additions & 4 deletions docs/AllMine outputs.rst
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Expand Up @@ -25,17 +25,17 @@ Mapped reads and de novo splicing junctions
Two different strategies of mapping are supported by AllMine. For DNA sequencing
inputs, AllMine uses BWA (Burrows-Wheeler Aligner). For RNA sequencing input,
STAR (Spliced Transcripts Alignment to a Reference) is used with a two pass
strategy. In both case, mapped and sorted reads are stored in the **mapped**
strategy. In both cases, mapped and sorted reads are stored in the **mapped**
directory. Both full alignments files and parsed around specified regions are
conserved, allowing new parsing around other regions without executing the
mapping one again. In the case of RNA sequencing data, the sub-directory
mapping once again. In the case of RNA sequencing data, the sub-directory
**STAR_SJ** is created. It contains the de novo splicing junctions discovered by
STAR during the first pass of the mapping.

Putative SNPs
-------------

Putative variants called by Varscan can be found in the **variant** directory.
Putative variants called by Annovar can be found in the **variant** directory.
Each subfolder correspond to one sample. Annotated, phased and raw variants are
displayed.

Expand All @@ -52,4 +52,4 @@ Run Report
----------

Allmine build an R markdown report to sum up most of the information about
the run. This report also include coverage plots for regions of interest.
the run. This report also include coverage plots for regions of interest.
2 changes: 1 addition & 1 deletion docs/Modules documentation.rst
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Expand Up @@ -110,7 +110,7 @@ Parameters :
* ``--scoreInsBase`` : Set to -2. Insertion extension penalty per base
(in addition to scoreInsOpen).
* ``--scoreStitchSJshift`` : Set to 1. Maximum score reduction while searching
for SJ boundaries inthe stitching step.
for SJ boundaries in the stitching step.
* ``--runThreadN`` : Set to 10. Number of threads used per jobs.

Note : STAR include numerous parameters, please read the manual for more
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14 changes: 7 additions & 7 deletions docs/Quick Start guide.rst
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Expand Up @@ -29,7 +29,7 @@ To perform allele mining, AllMine needs :

* Sequencing data (DNA or RNA)
* A reference genome and annotation
* A bed file with regions (or genes) of interests
* A bed file with regions (or genes) of interest

Sequencing data
---------------
Expand Down Expand Up @@ -65,8 +65,8 @@ Reference genome and annotation

Reference genome must be provided in one file, in **fasta format**.
Annotation can be provided in **gff** or **gtf** format (recommended).
When possible, we advice you to download reference sequence and annotation
from currated sources, such as `Ensembl <http://ensemblgenomes.org/>`_.
When possible, we advice you to download the reference sequence and annotation
from curated sources, such as `Ensembl <http://ensemblgenomes.org/>`_.

Bed file
--------
Expand All @@ -88,7 +88,7 @@ Making your work space ready
----------------------------

Place your reference genome and annotation in a common folder. That one must
only contain those both file. Place your bed file with regions of interest in
only contain those both files. Place your bed file with regions of interest in
an other folder. **AllMine outputs are created where your start the analysis.**
Make sure that you have enought space to store all outputs !

Expand All @@ -101,7 +101,7 @@ To configure an AllMine run use :
./csv_to_yaml.py path/to/sample_sheet.csv
Answer the question the script is asking you to configure your run.
Answer the questions the script is asking you to configure your run.
Note : the bind path is the path from the **root to your home folder.**

Once done run :
Expand All @@ -116,7 +116,7 @@ each new genome used.
Running AllMine
---------------

We recommend to first do a dry run using the following command.
We recommend first to do a dry run using the following command.
**CORE_NUMBER** must be replaced by the number of cores you wish to use.

.. code-block:: bash
Expand All @@ -126,7 +126,7 @@ We recommend to first do a dry run using the following command.
--cluster "sbatch" -n
Check the output to ensure that your run is properly configured.
If no, return to configurtion step to correct errors. If yes, run :
If not, return to configuration step to correct errors. If yes, run :

.. code-block:: bash
Expand Down
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6 changes: 3 additions & 3 deletions docs/_build/html/AllMine outputs.html
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Expand Up @@ -182,16 +182,16 @@ <h2>Mapped reads and de novo splicing junctions<a class="headerlink" href="#mapp
<p>Two different strategies of mapping are supported by AllMine. For DNA sequencing
inputs, AllMine uses BWA (Burrows-Wheeler Aligner). For RNA sequencing input,
STAR (Spliced Transcripts Alignment to a Reference) is used with a two pass
strategy. In both case, mapped and sorted reads are stored in the <strong>mapped</strong>
strategy. In both cases, mapped and sorted reads are stored in the <strong>mapped</strong>
directory. Both full alignments files and parsed around specified regions are
conserved, allowing new parsing around other regions without executing the
mapping one again. In the case of RNA sequencing data, the sub-directory
mapping once again. In the case of RNA sequencing data, the sub-directory
<strong>STAR_SJ</strong> is created. It contains the de novo splicing junctions discovered by
STAR during the first pass of the mapping.</p>
</div>
<div class="section" id="putative-snps">
<h2>Putative SNPs<a class="headerlink" href="#putative-snps" title="Permalink to this headline"></a></h2>
<p>Putative variants called by Varscan can be found in the <strong>variant</strong> directory.
<p>Putative variants called by Annovar can be found in the <strong>variant</strong> directory.
Each subfolder correspond to one sample. Annotated, phased and raw variants are
displayed.</p>
</div>
Expand Down
2 changes: 1 addition & 1 deletion docs/_build/html/Modules documentation.html
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Expand Up @@ -269,7 +269,7 @@ <h2>STAR; RNAseq reads mapping<a class="headerlink" href="#star-rnaseq-reads-map
<li><p><code class="docutils literal notranslate"><span class="pre">--scoreInsBase</span></code> : Set to -2. Insertion extension penalty per base
(in addition to scoreInsOpen).</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--scoreStitchSJshift</span></code> : Set to 1. Maximum score reduction while searching
for SJ boundaries inthe stitching step.</p></li>
for SJ boundaries in the stitching step.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">--runThreadN</span></code> : Set to 10. Number of threads used per jobs.</p></li>
</ul>
</div></blockquote>
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14 changes: 7 additions & 7 deletions docs/_build/html/Quick Start guide.html
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Expand Up @@ -186,7 +186,7 @@ <h2>Input files<a class="headerlink" href="#input-files" title="Permalink to thi
<div><ul class="simple">
<li><p>Sequencing data (DNA or RNA)</p></li>
<li><p>A reference genome and annotation</p></li>
<li><p>A bed file with regions (or genes) of interests</p></li>
<li><p>A bed file with regions (or genes) of interest</p></li>
</ul>
</div></blockquote>
</div>
Expand Down Expand Up @@ -217,8 +217,8 @@ <h2>Sample sheet<a class="headerlink" href="#sample-sheet" title="Permalink to t
<h2>Reference genome and annotation<a class="headerlink" href="#reference-genome-and-annotation" title="Permalink to this headline"></a></h2>
<p>Reference genome must be provided in one file, in <strong>fasta format</strong>.
Annotation can be provided in <strong>gff</strong> or <strong>gtf</strong> format (recommended).
When possible, we advice you to download reference sequence and annotation
from currated sources, such as <a class="reference external" href="http://ensemblgenomes.org/">Ensembl</a>.</p>
When possible, we advice you to download the reference sequence and annotation
from curated sources, such as <a class="reference external" href="http://ensemblgenomes.org/">Ensembl</a>.</p>
</div>
<div class="section" id="bed-file">
<h2>Bed file<a class="headerlink" href="#bed-file" title="Permalink to this headline"></a></h2>
Expand All @@ -236,7 +236,7 @@ <h2>Bed file<a class="headerlink" href="#bed-file" title="Permalink to this head
<div class="section" id="making-your-work-space-ready">
<h2>Making your work space ready<a class="headerlink" href="#making-your-work-space-ready" title="Permalink to this headline"></a></h2>
<p>Place your reference genome and annotation in a common folder. That one must
only contain those both file. Place your bed file with regions of interest in
only contain those both files. Place your bed file with regions of interest in
an other folder. <strong>AllMine outputs are created where your start the analysis.</strong>
Make sure that you have enought space to store all outputs !</p>
</div>
Expand All @@ -246,7 +246,7 @@ <h2>Configuration of an AllMine run<a class="headerlink" href="#configuration-of
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./csv_to_yaml.py path/to/sample_sheet.csv
</pre></div>
</div>
<p>Answer the question the script is asking you to configure your run.
<p>Answer the questions the script is asking you to configure your run.
Note : the bind path is the path from the <strong>root to your home folder.</strong></p>
<p>Once done run :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./annovar_makebd.py
Expand All @@ -257,15 +257,15 @@ <h2>Configuration of an AllMine run<a class="headerlink" href="#configuration-of
</div>
<div class="section" id="running-allmine">
<h2>Running AllMine<a class="headerlink" href="#running-allmine" title="Permalink to this headline"></a></h2>
<p>We recommend to first do a dry run using the following command.
<p>We recommend first to do a dry run using the following command.
<strong>CORE_NUMBER</strong> must be replaced by the number of cores you wish to use.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>snakemake -j CORE_NUMBER <span class="se">\</span>
--cluster-config slurm_config.json <span class="se">\</span>
--cluster <span class="s2">&quot;sbatch&quot;</span> -n
</pre></div>
</div>
<p>Check the output to ensure that your run is properly configured.
If no, return to configurtion step to correct errors. If yes, run :</p>
If not, return to configuration step to correct errors. If yes, run :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>snakemake -j CORE_NUMBER <span class="se">\</span>
--cluster-config slurm_config.json <span class="se">\</span>
--cluster <span class="s2">&quot;sbatch&quot;</span>
Expand Down
8 changes: 4 additions & 4 deletions docs/_build/html/_sources/AllMine outputs.rst.txt
View file
Expand Up @@ -25,17 +25,17 @@ Mapped reads and de novo splicing junctions
Two different strategies of mapping are supported by AllMine. For DNA sequencing
inputs, AllMine uses BWA (Burrows-Wheeler Aligner). For RNA sequencing input,
STAR (Spliced Transcripts Alignment to a Reference) is used with a two pass
strategy. In both case, mapped and sorted reads are stored in the **mapped**
strategy. In both cases, mapped and sorted reads are stored in the **mapped**
directory. Both full alignments files and parsed around specified regions are
conserved, allowing new parsing around other regions without executing the
mapping one again. In the case of RNA sequencing data, the sub-directory
mapping once again. In the case of RNA sequencing data, the sub-directory
**STAR_SJ** is created. It contains the de novo splicing junctions discovered by
STAR during the first pass of the mapping.

Putative SNPs
-------------

Putative variants called by Varscan can be found in the **variant** directory.
Putative variants called by Annovar can be found in the **variant** directory.
Each subfolder correspond to one sample. Annotated, phased and raw variants are
displayed.

Expand All @@ -52,4 +52,4 @@ Run Report
----------

Allmine build an R markdown report to sum up most of the information about
the run. This report also include coverage plots for regions of interest.
the run. This report also include coverage plots for regions of interest.
2 changes: 1 addition & 1 deletion docs/_build/html/_sources/Modules documentation.rst.txt
View file
Expand Up @@ -110,7 +110,7 @@ Parameters :
* ``--scoreInsBase`` : Set to -2. Insertion extension penalty per base
(in addition to scoreInsOpen).
* ``--scoreStitchSJshift`` : Set to 1. Maximum score reduction while searching
for SJ boundaries inthe stitching step.
for SJ boundaries in the stitching step.
* ``--runThreadN`` : Set to 10. Number of threads used per jobs.

Note : STAR include numerous parameters, please read the manual for more
Expand Down
14 changes: 7 additions & 7 deletions docs/_build/html/_sources/Quick Start guide.rst.txt
View file
Expand Up @@ -29,7 +29,7 @@ To perform allele mining, AllMine needs :

* Sequencing data (DNA or RNA)
* A reference genome and annotation
* A bed file with regions (or genes) of interests
* A bed file with regions (or genes) of interest

Sequencing data
---------------
Expand Down Expand Up @@ -65,8 +65,8 @@ Reference genome and annotation

Reference genome must be provided in one file, in **fasta format**.
Annotation can be provided in **gff** or **gtf** format (recommended).
When possible, we advice you to download reference sequence and annotation
from currated sources, such as `Ensembl <http://ensemblgenomes.org/>`_.
When possible, we advice you to download the reference sequence and annotation
from curated sources, such as `Ensembl <http://ensemblgenomes.org/>`_.

Bed file
--------
Expand All @@ -88,7 +88,7 @@ Making your work space ready
----------------------------

Place your reference genome and annotation in a common folder. That one must
only contain those both file. Place your bed file with regions of interest in
only contain those both files. Place your bed file with regions of interest in
an other folder. **AllMine outputs are created where your start the analysis.**
Make sure that you have enought space to store all outputs !

Expand All @@ -101,7 +101,7 @@ To configure an AllMine run use :
./csv_to_yaml.py path/to/sample_sheet.csv
Answer the question the script is asking you to configure your run.
Answer the questions the script is asking you to configure your run.
Note : the bind path is the path from the **root to your home folder.**

Once done run :
Expand All @@ -116,7 +116,7 @@ each new genome used.
Running AllMine
---------------

We recommend to first do a dry run using the following command.
We recommend first to do a dry run using the following command.
**CORE_NUMBER** must be replaced by the number of cores you wish to use.

.. code-block:: bash
Expand All @@ -126,7 +126,7 @@ We recommend to first do a dry run using the following command.
--cluster "sbatch" -n
Check the output to ensure that your run is properly configured.
If no, return to configurtion step to correct errors. If yes, run :
If not, return to configuration step to correct errors. If yes, run :

.. code-block:: bash
Expand Down
4 changes: 2 additions & 2 deletions docs/_build/html/_sources/index.rst.txt
View file
Expand Up @@ -5,7 +5,7 @@ AllMine Documentation
*********************

AllMine is a flexible allele mining pipeline. AllMine can handle various NGS
data types (WGS, RRGS, RNAseq, paired/sengle end layouts...) and process all
data types (WGS, RRGS, RNAseq, paired/single end layouts...) and process all
steps from raw reads to de novo SNPs phasing and annotation. Designed for easy
usage, AllMine can be use by non bioinformaticians. AllMine is HPC compatible
via Slurm.
Expand All @@ -22,7 +22,7 @@ Follow AllMine development on `GitHub <https://github.com/tbersez/Allmine>`_.
:caption: Contents:

Quick Start guide

AllMine outputs
Modules documentation
Dependancies
Expand Down
2 changes: 1 addition & 1 deletion docs/_build/html/index.html
View file
Expand Up @@ -153,7 +153,7 @@
<div class="section" id="allmine-documentation">
<h1>AllMine Documentation<a class="headerlink" href="#allmine-documentation" title="Permalink to this headline"></a></h1>
<p>AllMine is a flexible allele mining pipeline. AllMine can handle various NGS
data types (WGS, RRGS, RNAseq, paired/sengle end layouts…) and process all
data types (WGS, RRGS, RNAseq, paired/single end layouts…) and process all
steps from raw reads to de novo SNPs phasing and annotation. Designed for easy
usage, AllMine can be use by non bioinformaticians. AllMine is HPC compatible
via Slurm.</p>
Expand Down

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