annotate ezBAMQC/README.rst @ 18:494b5cd02238

bash script
author youngkim
date Wed, 30 Mar 2016 13:39:05 -0400
parents 6610eedd9fae
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
1 =======
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
2 ezBAMQC
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
3 =======
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
4
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
5 *"ezBAMQC, a tool to check the quality of mapped next generation sequencing files."*
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
6
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
7 :Codeology Icon:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
8
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
9 .. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.gif
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
10 :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
11 :align: right
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
12 :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
13
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
14 :Description:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
15
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
16 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.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
17
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
18 :Links:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
19
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
20 `Github Page <https://github.com/mhammell-laboratory/bamqc>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
21
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
22 `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
23
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
24 `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
25
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
26 :Authors:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
27 Ying Jin, David Molik, and Molly Hammell
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
28
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
29 :Version: 0.6.7
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
30
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
31 :Contact:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
32 Ying Jin (yjin@cshl.edu)
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
33
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
34 Installation guide for ezBAMQC for from source installs
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
35 =======================================================
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
36
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
37 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.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
38
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
39 :Intallation:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
40 `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
41
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
42 `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
43
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
44 :Prerequisites:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
45 * `python2.7 <https://www.python.org/download/releases/2.7/>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
46 * `R <https://www.r-project.org/>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
47 * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
48 * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
49
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
50 :Notes:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
51 * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
52 * `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
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
53 * `IUS <https://ius.io/>`_ for Python2.7
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
54 * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
55 * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
56
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
57 Setup
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
58 =====
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
59
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
60 1) Make sure that the GCC comiler is in your PATH:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
61
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
62 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
63
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
64 export PATH=/path/to/gcc:$PATH
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
65
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
66 2) Make sure that python2.7 is in your PYTHONPATH:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
67
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
68 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
69
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
70 export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
71
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
72 3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
73
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
74 From Source
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
75 ~~~~~~~~~~~
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
76
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
77 1) Download source
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
78
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
79 2) Unpack tarball and go to the directory of the package:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
80
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
81 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
82
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
83 tar xvfz bamqc-0.6.7.tar.gz
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
84
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
85 cd bamqc-0.6.7
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
86
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
87 3) Run make:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
88
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
89 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
90
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
91 make
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
92
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
93 From Setup.py
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
94 ~~~~~~~~~~~~~
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
95
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
96 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
97
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
98 python2.7 setup.py install
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
99
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
100 From Pypi
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
101 ~~~~~~~~~
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
102
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
103 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
104
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
105 pip2.7 install BAMqc
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
106
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
107 Usage
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
108 =====
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
109
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
110 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
111
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
112 ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
113 [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
114 [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
115
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
116 optional arguments:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
117
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
118 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
119
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
120 -h, --help show this help message and exit.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
121 -i, --inputFile alignment files. Could be multiple SAM/BAM files separated by space. Required.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
122 -r, --refgene gene annotation file in GTF format. Required
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
123 -f the read summation at which feature level in the GTF file. DEFAULT: gene_id.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
124 --rRNA rRNA coordinates in BED format.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
125 -o, --outputDir output directory. Required.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
126 --stranded strandness of the library?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
127 yes : sense stranded
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
128 reverse : reverse stranded
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
129 no : not stranded
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
130 DEFAULT: yes.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
131 -q, --mapq Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
132 -l, --label Labels of input files. DEFAULT:smp1 smp2 ...
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
133 -t, --threads Number of threads to use. DEFAULT:1
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
134
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
135 Example:
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
136
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
137 ::
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
138
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
139 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
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
140
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
141 Please find the example output from folder test-data.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
142
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
143 FAQ
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
144 ===
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
145 Q: Why use ezBAMQC?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
146
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
147 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.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
148
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
149 Q: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
150
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
151 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.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
152
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
153 Q: What is "Low Quality Reads" ?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
154
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
155 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".
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
156
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
157 Q: How the setting of option -q alter the results?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
158
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
159 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.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
160
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
161 Q: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
162
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
163 A: No. Only uniquely mapped reads were counted.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
164
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
165
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
166 Acknowledgements
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
167 ================
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
168
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
169 #) Samtools contributors
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
170 #) Users' valuable feedback
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
171
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
172 Copying & Distribution
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
173 ======================
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
174
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
175 ezBAMQC is free software: you can redistribute it and/or modify
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
176 it under the terms of the GNU General Public License as published by
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
177 the Free Software Foundation, either version 3 of the License, or
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
178 (at your option) any later version.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
179
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
180 This program is distributed in the hope that it will be useful,
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
181 but *WITHOUT ANY WARRANTY*; without even the implied warranty of
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
182 *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*. See the
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
183 GNU General Public License for more details.
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
184
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
185 You should have received a copy of the GNU General Public License
6610eedd9fae Uploaded
cshl-bsr
parents: 0
diff changeset
186 along with ezBAMQC. If not, see `this website <http://www.gnu.org/licenses/>`_