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| diff -r 773b3a97d43c -r aeac72f23524 README.rst --- a/README.rst Tue Mar 29 16:51:06 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,186 +0,0 @@ -======= -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/>`_ |