{
    "info": {
        "author": "Ying Jin",
        "author_email": "yjin@cshl.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Natural Language :: English",
            "Operating System :: Unix",
            "Programming Language :: C++",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "=======\r\nezBAMQC\r\n=======\r\n\r\n*\"ezBAMQC, a tool to check the quality of mapped next generation sequencing files.\"*\r\n\r\n:Codeology Icon:\r\n\r\n   .. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.gif\r\n     :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc\r\n     :align: right\r\n     :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc\r\n\r\n:Description:\r\n\r\n   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\u2019 and 3\u2019 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.\r\n\r\n:Links:\r\n\r\n    `Github Page <https://github.com/mhammell-laboratory/bamqc>`_\r\n\r\n    `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_\r\n\r\n    `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_\r\n\r\n:Authors:\r\n    Ying Jin, David Molik, and Molly Hammell\r\n\r\n:Version: 0.6.7\r\n\r\n:Contact:\r\n    Ying Jin (yjin@cshl.edu)\r\n\r\nInstallation guide for ezBAMQC for from source installs\r\n=======================================================\r\n\r\nWhen 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.\r\n\r\n:Intallation:\r\n   `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_\r\n\r\n   `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_\r\n\r\n:Prerequisites:\r\n    * `python2.7 <https://www.python.org/download/releases/2.7/>`_\r\n    * `R <https://www.r-project.org/>`_\r\n    * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_\r\n    * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install \r\n\r\n:Notes:\r\n    * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*\r\n    * `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\r\n    * `IUS <https://ius.io/>`_ for Python2.7\r\n    * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)\r\n    * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems\r\n\r\nSetup\r\n=====\r\n\r\n1) Make sure that the GCC comiler is in your PATH:\r\n\r\n::\r\n\r\n   export PATH=/path/to/gcc:$PATH\r\n\r\n2) Make sure that python2.7 is in your PYTHONPATH:\r\n\r\n::\r\n\r\n   export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH\r\n\r\n3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. \r\n\r\nFrom Source\r\n~~~~~~~~~~~\r\n\r\n1) Download source \r\n\r\n2) Unpack tarball and go to the directory of the package: \r\n\r\n::\r\n\r\n   tar xvfz bamqc-0.6.7.tar.gz\r\n\r\n   cd bamqc-0.6.7\r\n\r\n3) Run make:\r\n\r\n::\r\n\r\n   make\r\n\r\nFrom Setup.py\r\n~~~~~~~~~~~~~\r\n\r\n::\r\n\r\n   python2.7 setup.py install \r\n\r\nFrom Pypi\r\n~~~~~~~~~\r\n\r\n::\r\n\r\n   pip2.7 install BAMqc\r\n\r\nUsage\r\n=====\r\n\r\n::\r\n\r\n   ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]\r\n   [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]\r\n   [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]\r\n\r\noptional arguments:\r\n\r\n::\r\n\r\n   -h, --help               show this help message and exit.\r\n   -i, --inputFile          alignment files. Could be multiple SAM/BAM files separated by space. Required.\r\n   -r, --refgene            gene annotation file in GTF format. Required\r\n   -f                       the read summation at which feature level in the GTF file. DEFAULT: gene_id.\r\n   --rRNA                   rRNA coordinates in BED format.\r\n   -o, --outputDir          output directory. Required.\r\n   --stranded               strandness of the library? \r\n                            yes : sense stranded\r\n                            reverse : reverse stranded\r\n                            no : not stranded\r\n                            DEFAULT: yes.\r\n   -q, --mapq               Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30\r\n   -l, --label              Labels of input files. DEFAULT:smp1 smp2 ...\r\n   -t, --threads            Number of threads to use. DEFAULT:1\r\n\r\nExample: \r\n\r\n::\r\n\r\n   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\r\n\r\n   Please find the example output from folder test-data.\r\n\r\nDemo\r\n====\r\n\r\nWant to try ezBAMQC before trying it? you can now utilize our tool demo hosted on our `Yabi Demo <https://demo.bsr.tools/yabi>`_ to do so.\r\n\r\n+------------------------------------+\r\n|To login use username and password: |\r\n+====================================+\r\n|- username: **tdemo**               |\r\n|- password: **tdemo**               |\r\n+------------------------------------+\r\n\r\n.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-login.png\r\n  :alt: The BSR/MHammell lab yabi installation\r\n  :align: center\r\n  :target: https://demo.bsr.tools/yabi\r\n\r\nThe login screen, usernname and password go in the top right corner.\r\n\r\n.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-show-all.png\r\n  :alt: The BSR/MHammell lab yabi installation\r\n  :align: center\r\n  :target: https://demo.bsr.tools/yabi\r\n\r\nThe \"Design\" Frame, use the \"show all\" button to make visable the ezBAMQC tool.\r\n\r\n.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-show-files.png\r\n  :alt: The BSR/MHammell lab yabi installation\r\n  :align: center\r\n  :target: https://demo.bsr.tools/yabi\r\n\r\nThe ezBAMQC tool page, select appropriate files from the S3 instance or upload your own. \r\n\r\n  *A note on Yabi, Yabi was created by the Centre For Comparative Genomics, https://ccg.murdoch.edu.au/ . You can check our their more extensive Yabi Demo, https://ccgapps.com.au/yabi/ or their Yabi Wiki, https://bitbucket.org/ccgmurdoch/yabi/wiki/Home for more information.*\r\n\r\nFAQ\r\n===\r\nQ: Why use ezBAMQC?\r\n\r\nA: 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.\r\n\r\nQ: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?\r\n\r\nA: 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. \r\n\r\nQ: What is \"Low Quality Reads\" ?\r\n\r\nA: 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\".\r\n\r\nQ: How the setting of option -q alter the results? \r\n\r\nA: 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. \r\n\r\nQ: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?\r\n\r\nA: No. Only uniquely mapped reads were counted. \r\n\r\n\r\nAcknowledgements\r\n================\r\n\r\n#) Samtools contributors\r\n#) Users' valuable feedback\r\n\r\nCopying & Distribution\r\n======================\r\n\r\nezBAMQC is free software: you can redistribute it and/or modify\r\nit under the terms of the GNU General Public License as published by\r\nthe Free Software Foundation, either version 3 of the License, or\r\n(at your option) any later version.\r\n\r\nThis program is distributed in the hope that it will be useful,\r\nbut *WITHOUT ANY WARRANTY*; without even the implied warranty of\r\n*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*.  See the\r\nGNU General Public License for more details.\r\n\r\nYou should have received a copy of the GNU General Public License\r\nalong with ezBAMQC.  If not, see `this website <http://www.gnu.org/licenses/>`_",
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