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ezBAMQC-0.6.7
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Quality control tools for NGS alignment file
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | ezBAMQC-0.6.7 |
| نام | ezBAMQC |
| نسخه کتابخانه | 0.6.7 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Ying Jin |
| ایمیل نویسنده | yjin@cshl.edu |
| آدرس صفحه اصلی | http://hammelllab.labsites.cshl.edu/software#BAMqc |
| آدرس اینترنتی | https://pypi.org/project/ezBAMQC/ |
| مجوز | GPLv3 |
=======
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.
Demo
====
Want 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.
+------------------------------------+
|To login use username and password: |
+====================================+
|- username: **tdemo** |
|- password: **tdemo** |
+------------------------------------+
.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-login.png
:alt: The BSR/MHammell lab yabi installation
:align: center
:target: https://demo.bsr.tools/yabi
The login screen, usernname and password go in the top right corner.
.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-show-all.png
:alt: The BSR/MHammell lab yabi installation
:align: center
:target: https://demo.bsr.tools/yabi
The "Design" Frame, use the "show all" button to make visable the ezBAMQC tool.
.. image:: https://raw.githubusercontent.com/mhammell-laboratory/ezBAMQC/master/doc/demo-show-files.png
:alt: The BSR/MHammell lab yabi installation
:align: center
:target: https://demo.bsr.tools/yabi
The ezBAMQC tool page, select appropriate files from the S3 instance or upload your own.
*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.*
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/>`_
نحوه نصب
نصب پکیج whl ezBAMQC-0.6.7:
pip install ezBAMQC-0.6.7.whl
نصب پکیج tar.gz ezBAMQC-0.6.7:
pip install ezBAMQC-0.6.7.tar.gz