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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| psr_v_1.1.tar.gz | 2015-10-12 | 19.7 kB | |
| README.txt | 2015-10-12 | 6.9 kB | |
| psr_v_1.0.tar.gz | 2015-05-26 | 19.9 kB | |
| Totals: 3 Items | 46.5 kB | 1 |
Last updated on: 02/09/2015 PSR (Polymorphic SSR Retrieval ) user manual. The following inaccuracies were fixed in this version: - The DESTROY object method for Bio::DB::Sam instance has been deprecated in PSR_read_retrieval.pl - In PSR_poly_finder.pl script the mysql user, named psr, writes the query result on server host by setting FILE privilege, then the file is moved to the folder of user's choice. Contents: 1. LICENSE 2. OBTAINING PSR 3. REQUIREMENTS 4. INSTALLATION 5. INPUT FILES 6. RUNNING PSR 7. OUTPUT FILES ######################################################################################## 1. LICENSE PSR is a computational tool to identify polymorphic microsatellites from NGS data. This program is free: 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 this program. If not, see http://www.gnu.org/licenses/. AUTHORS: Concita Cantarella Nunzio D'Agostino Contact: concita.cantarella@gmail.com nunzio.dagostino@entecra.it Reference: PSR: polymorphic SSR retrieval. Cantarella C., D'Agostino N. BMC Research Notes 2015, 8:525 doi:10.1186/s13104-015-1474-4 ######################################################################################## 2. OBTAINING PSR PSR is an open source program that can be freely downloaded from: https://sourceforge.net/projects/polyssr/ ######################################################################################## 3. REQUIREMENTS PSR has been completely developed using Perl v5.10.1. In order to run PSR, prior installation of Perl (5.10 or higher version) and MYSQL (5.5.23 or higher version) are required. Although PSR has been developed on Unix systems, it is compatible with all Unix and MS Windows based operating systems. Mandatory Perl modules: Text::CSV Bio::DB::Sam DBD::SQLite Module::Build File:Which Math::Random SOAP::Lite Sort::Naturally Array::Compare DBI DBD::mysql Mandatory SAMtools available at http://samtools.sourceforge.net (If an error occurs during installation try to add option –fPIC for CFLAGS in Makefile and Makefile.mingw) The follow command line allows to install older and stable version of required Bio::DB::Sam module. $ cpanm Bio::DB::Sam~">= 1.38, < 1.41" ######################################################################################## 4. INSTALLATION PSR is run directly using source files so it does not need to be configured with system. Simple unpacking of the downloaded files will be sufficient in order to complete the installation step. 4.1 Unpacking: For Unix: tar -xvzf psr.tar.gz For Windows based systems: psr.zip can be unpacked using Winzip or Winrar utilities. 4.2 Directory structure Unpacking of PSR will result in the main program directory. Directory structure and package distribution is as follows: -scripts folder -README file -LICENSE file --------MANDATORY-------- It is need special privileges to create or to delete a MySQL database. So assuming you have access to the root user, before running PSR scripts, you have to create a new database named 'PSR_DB' and a new mysql user named 'psr' able to read and write tables in PSR_DB and having FILE privileges. You could access the MySQL shell and typing the following command into terminal mysql> CREATE DATABASE PSR_DB mysql> GRANT ALL PRIVILEGES ON PSR_DB.* To 'psr'@'localhost'; mysql> GRANT FILE ON *.* TO 'psr'@'localhost'; ######################################################################################## 5. INPUT FILES (a.) PSR_read_retrieval.pl 1) Tab delimited file with 7 columns. It is a MISA-like output file (http://pgrc.ipk-gatersleben.de/misa/misa.html) which includes: ID SSR nr. SSR type SSR size start end transcript1 1 p3 (AGG)5 15 3967 3981 transcript1 2 p1 (T)13 13 4968 4982 transcript2 1 p2 (AC)7 14 11452 11465 2) BAM file storing read alignments against reference sequences for each genotype under investigation At the moment, with this PSR version, we suggest to use bowtie2 as mapping alignment tool. The option --very-sensitive and --end-to-end mode could be used to set the entire read alignment (expecially SSR flanking region) and no mismatches. The option -a searches for and reports all alignments position for each read. (b.) PSR_poly_finder.pl 1) One PSR_counts.txt file for each sample. This file is generated by PSR_read_retrieval.pl. ######################################################################################## 6. RUNNING PSR PSR is a standalone command line program that is run either using shell (on Unix system) or command prompt/DOS (on Windows system). Command line: perl PSR_read_retrieval.pl -m <tab-separeted file> -d <directory with BAM > -o <output directory> [-t minimum read depth] [-p polymorphism percentage depth] Where: -m File storing the localization and type of the identified microsatellites ( see PSR_read_retrieval.pl INPUT file) -d The directory containing one or more bam files resulting from read alignment versus reference sequences -o A directory where all the output files will be written. To create a new directory on Unix based systems: mkdir <new_directory_name> -t Minimum read depth -p Minimum supporting reads (% of aligning reads) at a position to call variants perl PSR_poly_finder.pl -i <input folder> -o <output directory > Where: -i The directory containing PSR_counts.txt files. -o A directory where output files will be written. ######################################################################################## 7. OUTPUT FILES (a.) PSR_read_retrieval.pl PSR_counts.txt Object SSR start stop # repeat unit # reads transcript1 (AG)8 502 517 8 150 transcript1 (AG)8 502 517 9 74 transcript2 (T)16 542 557 12 1000 transcript3 (T)12 550 561 13 423 (b.) PSR_poly_finder.pl PSR_polySSR_date.txt Seq_ID SSR start stop sample1 sample2 transcript1 (TC)8 1064 1079 5 0 transcript2 (TC)8 1052 1067 8 0 transcript3 (A)10 282 291 10 10 transcript4 (TTC)6 32 49 6;4 5 PSR_polySSR_date.txt is a tab delimited file written in /tmp/ folder or a folder selected by the user via commandline. In order to build the resulting table, the PSR_poly_finder.pl script creates several mysql temporary tables, two for each sample, and one overall table.
