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--- a/ezBAMQC/README.rst	Wed Mar 30 12:03:10 2016 -0400
+++ b/ezBAMQC/README.rst	Wed Mar 30 12:11:46 2016 -0400
@@ -1,184 +1,186 @@
-.. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.png
-   :width: 200 px
-   :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
-   :align: right
-   :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc
-
-=====
-ezBAMQC
-=====
-*"ezBAMQC, a tool to check the quality of mapped next generation sequencing files."*
-
-:Description:
-
-   ezBAMQC is a tool to check the quality of either one or many mapped next-generation-sequencing datasets. It conducts comprehensive evaluations of aligned sequencing data from multiple aspects including: clipping profile, mapping quality distribution, mapped read length distribution, genomic/transcriptomic mapping distribution, inner distance distribution (for paired-end reads), ribosomal RNA contamination, transcript 5’ and 3’ end bias, transcription dropout rate, sample correlations, sample reproducibility, sample variations. It outputs a set of tables and plots and one HTML page that contains a summary of the results. Many metrics are designed for RNA-seq data specifically, but ezBAMQC can be applied to any mapped sequencing dataset such as RNA-seq, CLIP-seq, GRO-seq, ChIP-seq, DNA-seq and so on. ::
-
-:Links:
-
-    `Github Page <https://github.com/mhammell-laboratory/bamqc>`_
-
-    `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_
-
-    `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
-
-:Authors:
-    Ying Jin, David Molik, and Molly Hammell
-
-:Version: 0.6.5
-
-:Contact:
-    Ying Jin (yjin@cshl.edu)
-
-Installation guide for ezBAMQC for from source installs
-=====================================================
-
-When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you'll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you'll need Python, R and Corrplot for interfacing with the C code.
-
-:Intallation:
-   `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_
-
-   `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_
-
-:Prerequisites:
-    * `python2.7 <https://www.python.org/download/releases/2.7/>`_
-    * `R <https://www.r-project.org/>`_
-    * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
-    * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install 
-
-:Notes:
-    * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
-    * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
-    * `IUS <https://ius.io/>`_ for Python2.7
-    * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
-    * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
-
-Setup
-=====
-
-1) Make sure that the GCC comiler is in your PATH:
-
-::
-
-   export PATH=/path/to/gcc:$PATH
-
-2) Make sure that python2.7 is in your PYTHONPATH:
-
-::
-
-   export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
-
-3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. 
-
-From Source
-~~~~~~~~~~~
-
-1) Download source 
-
-2) Unpack tarball and go to the directory of the package: 
-
-::
-
-   tar xvfz bamqc-0.6.6.tar.gz
-
-   cd bamqc-0.6.6
-
-3) Run make:
-
-::
-
-   make
-
-From Setup.py
-~~~~~~~~~~~~~
-
-::
-
-   python2.7 setup.py install 
-
-From Pypi
-~~~~~~~~~
-
-::
-
-   pip2.7 install BAMqc
-
-Usage
-=====
-
-::
-
-   ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]
-   [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]
-   [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]
-
-optional arguments:
-
-::
-
-   -h, --help               show this help message and exit.
-   -i, --inputFile          alignment files. Could be multiple SAM/BAM files separated by space. Required.
-   -r, --refgene            gene annotation file in GTF format. Required
-   -f                       the read summation at which feature level in the GTF file. DEFAULT: gene_id.
-   --rRNA                   rRNA coordinates in BED format.
-   -o, --outputDir          output directory. Required.
-   --stranded               strandness of the library? 
-                            yes : sense stranded
-                            reverse : reverse stranded
-                            no : not stranded
-                            DEFAULT: yes.
-   -q, --mapq               Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30
-   -l, --label              Labels of input files. DEFAULT:smp1 smp2 ...
-   -t, --threads            Number of threads to use. DEFAULT:1
-
-Example: 
-
-::
-
-   ezBAMQC -i test-data/exp_data/treat1.bam test-data/exp_data/treat2.bam test-data/exp_data/treat3.bam -r test-data/exp_data/hg9_refGene.gtf -q 30 --rRNA test-data/exp_data/hg19_rRNA.bed -o exp_output2
-
-   Please find the example output from folder test-data.
-
-FAQ
-====
-Q: Why use ezBAMQC?
-
-A: ezBAMQC is efficient and easy to use. With one command line, it reports a comprehensive evaluation of the data with a set of plots and tables.The ability to assess multiple samples together with high efficiency make it especially useful in cases where there are a large number of samples from the same condition, genotype, or treatment. ezBAMQC was written in C++ and supports multithreading. A mouse RNA-seq sample with 120M alignments can be done in 8 minutes with 5 threads.
-
-Q: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?
-
-A: The difference is because of non-uniquely mapped reads or multiply aligned reads (multi-reads). Samtools flagstat counts each multiple aligment as a different reads, but ezBAMQC counts reads accoriding to the read ID, i.e., each individual read will be counted once no matter that it is a uniquely mapped read or multi-read. 
-
-Q: What is "Low Quality Reads" ?
-
-A: Reads marked as qc fail accoriding to SAM format or reads with mapping quality lower than the value set by the option -q will be considered as "Low Quality Reads".
-
-Q: How the setting of option -q alter the results? 
-
-A: Reads with low quality, i.e., did not pass -q cutoff, are only counted in Total Reads, Mapped Reads, and Mappability by mapping quality plot. The rest of the report does not include low quality reads. 
-
-Q: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?
-
-A: No. Only uniquely mapped reads were counted. 
-
-
-Acknowledgements
-================
-
-#) Samtools contributors
-#) Users' valuable feedback
-
-Copying & Distribution
-======================
-
-ezBAMQC is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but *WITHOUT ANY WARRANTY*; without even the implied warranty of
-*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with ezBAMQC.  If not, see `this website <http://www.gnu.org/licenses/>`_
+=======
+ezBAMQC
+=======
+
+*"ezBAMQC, a tool to check the quality of mapped next generation sequencing files."*
+
+:Codeology Icon:
+
+   .. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.gif
+     :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
+     :align: right
+     :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc
+
+:Description:
+
+   ezBAMQC is a tool to check the quality of either one or many mapped next-generation-sequencing datasets. It conducts comprehensive evaluations of aligned sequencing data from multiple aspects including: clipping profile, mapping quality distribution, mapped read length distribution, genomic/transcriptomic mapping distribution, inner distance distribution (for paired-end reads), ribosomal RNA contamination, transcript 5’ and 3’ end bias, transcription dropout rate, sample correlations, sample reproducibility, sample variations. It outputs a set of tables and plots and one HTML page that contains a summary of the results. Many metrics are designed for RNA-seq data specifically, but ezBAMQC can be applied to any mapped sequencing dataset such as RNA-seq, CLIP-seq, GRO-seq, ChIP-seq, DNA-seq and so on.
+
+:Links:
+
+    `Github Page <https://github.com/mhammell-laboratory/bamqc>`_
+
+    `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_
+
+    `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
+
+:Authors:
+    Ying Jin, David Molik, and Molly Hammell
+
+:Version: 0.6.7
+
+:Contact:
+    Ying Jin (yjin@cshl.edu)
+
+Installation guide for ezBAMQC for from source installs
+=======================================================
+
+When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you'll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you'll need Python, R and Corrplot for interfacing with the C code.
+
+:Intallation:
+   `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_
+
+   `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_
+
+:Prerequisites:
+    * `python2.7 <https://www.python.org/download/releases/2.7/>`_
+    * `R <https://www.r-project.org/>`_
+    * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
+    * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install 
+
+:Notes:
+    * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
+    * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
+    * `IUS <https://ius.io/>`_ for Python2.7
+    * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
+    * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
+
+Setup
+=====
+
+1) Make sure that the GCC comiler is in your PATH:
+
+::
+
+   export PATH=/path/to/gcc:$PATH
+
+2) Make sure that python2.7 is in your PYTHONPATH:
+
+::
+
+   export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
+
+3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. 
+
+From Source
+~~~~~~~~~~~
+
+1) Download source 
+
+2) Unpack tarball and go to the directory of the package: 
+
+::
+
+   tar xvfz bamqc-0.6.7.tar.gz
+
+   cd bamqc-0.6.7
+
+3) Run make:
+
+::
+
+   make
+
+From Setup.py
+~~~~~~~~~~~~~
+
+::
+
+   python2.7 setup.py install 
+
+From Pypi
+~~~~~~~~~
+
+::
+
+   pip2.7 install BAMqc
+
+Usage
+=====
+
+::
+
+   ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]
+   [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]
+   [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]
+
+optional arguments:
+
+::
+
+   -h, --help               show this help message and exit.
+   -i, --inputFile          alignment files. Could be multiple SAM/BAM files separated by space. Required.
+   -r, --refgene            gene annotation file in GTF format. Required
+   -f                       the read summation at which feature level in the GTF file. DEFAULT: gene_id.
+   --rRNA                   rRNA coordinates in BED format.
+   -o, --outputDir          output directory. Required.
+   --stranded               strandness of the library? 
+                            yes : sense stranded
+                            reverse : reverse stranded
+                            no : not stranded
+                            DEFAULT: yes.
+   -q, --mapq               Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30
+   -l, --label              Labels of input files. DEFAULT:smp1 smp2 ...
+   -t, --threads            Number of threads to use. DEFAULT:1
+
+Example: 
+
+::
+
+   ezBAMQC -i test-data/exp_data/treat1.bam test-data/exp_data/treat2.bam test-data/exp_data/treat3.bam -r test-data/exp_data/hg9_refGene.gtf -q 30 --rRNA test-data/exp_data/hg19_rRNA.bed -o exp_output2
+
+   Please find the example output from folder test-data.
+
+FAQ
+===
+Q: Why use ezBAMQC?
+
+A: ezBAMQC is efficient and easy to use. With one command line, it reports a comprehensive evaluation of the data with a set of plots and tables.The ability to assess multiple samples together with high efficiency make it especially useful in cases where there are a large number of samples from the same condition, genotype, or treatment. ezBAMQC was written in C++ and supports multithreading. A mouse RNA-seq sample with 120M alignments can be done in 8 minutes with 5 threads.
+
+Q: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?
+
+A: The difference is because of non-uniquely mapped reads or multiply aligned reads (multi-reads). Samtools flagstat counts each multiple aligment as a different reads, but ezBAMQC counts reads accoriding to the read ID, i.e., each individual read will be counted once no matter that it is a uniquely mapped read or multi-read. 
+
+Q: What is "Low Quality Reads" ?
+
+A: Reads marked as qc fail accoriding to SAM format or reads with mapping quality lower than the value set by the option -q will be considered as "Low Quality Reads".
+
+Q: How the setting of option -q alter the results? 
+
+A: Reads with low quality, i.e., did not pass -q cutoff, are only counted in Total Reads, Mapped Reads, and Mappability by mapping quality plot. The rest of the report does not include low quality reads. 
+
+Q: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?
+
+A: No. Only uniquely mapped reads were counted. 
+
+
+Acknowledgements
+================
+
+#) Samtools contributors
+#) Users' valuable feedback
+
+Copying & Distribution
+======================
+
+ezBAMQC is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but *WITHOUT ANY WARRANTY*; without even the implied warranty of
+*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with ezBAMQC.  If not, see `this website <http://www.gnu.org/licenses/>`_