README file for CUI verion of the QUMA 10/22/2010
ABSTRACT:
QUMA (QUantification tool for Methylation Analysis) is interactive and
easy-to-use web-based tool for the bisulfite sequencing analysis of
CpG methylation. The CUI version is character-based user interface version
of QUMA functions.
COPYRIGHT INFO:
The QUMA CUI version is copyright 2010-2012, Yuichi Kumaki. This is
released under the GNU General Public License (GPLv3)
These programs are 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.
These programs are 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 these programs. If not, see .
PREREQUISITES:
The QUMA CUI version is written in Perl and can be installed locally.
We tested that the QUMA can work at many Linux distributions, Mac OS X and
Windows 2000/XP (with cygwin), and will probably work at any UNIX-like OS.
(1) Perl open source scripting language
You need version 5.6.0 or higher.
(2) Perl modules
(a) Statistics-Lite
(3) needle program of the EMBOSSS software package
SETTING UP:
If perl is not located at /usr/bin/perl, please change the first line of quma.pl
If needle program is not located in your searchable path, please change the 32th
line of quma.pl to full path of the needle.
USAGE:
./quma.pl [options] - or input_file or -g genome_file -q query_file
Input data
1) - (STDIN)
Multi-FASTA format of genomic DNA sequence and bisulfite sequences
First sequence must be genomic DNA seuqnce
2) input_file
Multi-FASTA format of genomic DNA sequence and bisulfite sequences
First sequence must be genomic DNA seuqnce
3) -g genome_file -q query_file
genome_file : FASTA format genomic DNA sequence
query_file: Multi-FASTA format bisulfite sequences
Option
-f: output format (0|1|2|3) default 0
0: tab separated data
first line : 'genome', condition of convert direction (see below),
genomic sequence, number of CpG, CpG position (first base = 0)
other lines: No., sequence name, sequence, alignment data of this sequnece,
alignment data of genome sequence, alignment length,
number of alignmnet mismatch, percent identity of alignment,
number of alignment gap, number of methylated CpG,
number of bisulfite unconverted CpH (CpH: CpA, CpC, CpT),
number of bisulfite converted CpH,
percent of bisulfite convertion,
CpG methylation pattern (0: unmethylated, 1: methylated),
convert direction (1: forward, -1: reverse)
1: human readable alignment data
2: tab separated multiple alignment data
3: tab separated summarized data
-d: condition of convert direction of genomic sequence (0|1|2) default 0
0: C -> T conversion
PCR primer pair was designded for forward strand of the genomic sequence
1: G -> A conversion
PCR primer pair was designded for reverse strand of the genomic sequence
2: both
Search both direction of conversion and adopt more appropriate strand
-u: upper limit of unconverted CpHs (integer, default 5)
(CpH: CpA, CpC, CpT)
-c: lower limit of percent converted CpHs (float, default 95.0)
-m: upper limit of alignment mismatches (integer, default 10)
-p: lower limit of percent identity (float, default 90.0)
-u, -c, -m -p options are only affected output format 3 or 4
Example:
./quma.pl -g genomic_sequnce -q bisulfite_sequences -f 3 > output_file.txt
./input_data_generator.pl | ./quma.pl - | ./data_parser.pl
WHAT'S NEW:
10/22/2010 1.0.0
First version.
CONTACT:
Yuichi Kumaki & Masaki Okano
Laboratory for Mammalian Epigenetic Studies,
Center for Developmental Biology, RIKEN
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
quma@cdb.riken.jp
REFERENCE:
QUMA: quantification tool for methylation analysis
Yuichi Kumaki, Masaaki Oda & Masaki Okano*, Nucleic Acids Res. 36, W170-W175 (2008).
PubMed Central ID: PMC2447804, PubMed ID: 18487274
Laboratory for Mammalian Epigenetic Studies,
Center for Developmental Biology, RIKEN,
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
*To whom correspondence should be addressed.
Correspondence may also be addressed to Yuichi Kumaki.
Present address for Masaaki Oda:
Laboratory of Developmental Genetics and Imprinting,
The Babraham Institute, Cambridge CB22 3AT, UK
ACKNOWLEDGEMENTS:
We thank Akiko Yamagiwa for sample bisulfite sequences of the mouse
Gm9 region (1), Morito Sakaue and Masahumi Kawaguchi for constructive
feedback on the website, Hazuki S. Hiraga for proofreading of the
web site, Yoko Dote for helpful feedback on the "Terms of Use"
section, and the Information Networks Office of RIKEN Kobe Institute
for helpful suggestions in setting up the Internet connection for
the server. This work was supported in part by Grants-in-Aid from
the Ministry of Education, Culture, Sports, Science, and Technology
of Japan to M. Okano.
(1) Oda, M., Yamagiwa, A., Yamamoto, S., Nakayama, T., Tsumura, A.,
Sasaki, H., Nakao, K., Li, E. and Okano, M.
DNA methylation regulates long-range gene silencing of an
X-linked homeobox gene cluster in a lineage-specific manner.
Genes & Development, 20, 3382-3394 (2006).
AUTHOR:
Yuichi Kumaki
yuichi@kumaki.jp
Laboratory for Mammalian Epigenetic Studies,
Center for Developmental Biology, RIKEN,
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.