ferrolad / raca Goto Github PK
View Code? Open in Web Editor NEWThis project forked from ma-compbio/raca
License: MIT License
This project forked from ma-compbio/raca
License: MIT License
RACA (Reference-Assisted Chromosome Assembly) ============================================= This is the version used in the original PNAS paper. 0. Warning ---------- Please do not use a '.' symbol as a part of a chromosome name. The '.' symbol is used as a delimiter to separate a species name and a chromosome name in output files. If the '.' symbol is already in a chromosome name in your sequence files, please convert it to other symbol, like '_', before creating the chain/net files and read mapping files. 1. How to compile? ------------------ Just type 'make' to compile the RACA package. 2. How to run? -------------- 2.1 Configuration file RACA requires a single configuration file as a parameter. The configuration file has all parameters that are needed for RACA. Example dataset below has a sample configuration file 'params.txt' and all other parameter files which are self-explanatory. (also refer to the data directory.) Please read carefully the description of each configuration variable and modify them as needed. 2.2 Run RACA There is a wrapper Perl script, 'Run_RACA.pl'. To run RACA, type as: <path to RACA>/Run_RACA.pl <path to the configuration file> 3. Example dataset (Tibetan antelope assembly) ---------------------------------------------- 3.1 Download the dataset Visit http://bioinfo.konkuk.ac.kr/RACA/ and click the link "Tibetan antelope (TA) data". Then you can download the file TAdata.tgz file. 3.2 Compile the dataset Go into the directory where you downloaded the TAdata.tgz file and run: tar xvfz TAdata.tgz cd TAdata/ make 3.3 Run RACA for the dataset In the TAdata directory run: <path to RACA>/Run_RACA.pl params.txt 3.4 Where are output files? In the TAdata/Out_RACA directory. 4. What are produced? --------------------- In the output directory that is specified in the above configuration file, the following files are produced. - rec_chrs.refined.txt This file contains the order and orientation of target scaffolds in each reconstructed RACA chromosome fragment. Each column is defined as: Column1: the RACA chromosome fragment id Column2: start position (0-based) in the RACA chromosome fragment Column3: end position (1-based) in the RACA chromosome fragment Column4: target scaffold id or 'GAPS' Column5: start position (0-based) in the target scaffold Column6: end position (1-based) in the target scaffold - rec_chrs.<ref_spc>.segments.refined.txt This file contains the mapping between the RACA chromosome fragments and the genome sequences of the reference species <ref_spc>. - ref_chrs.<tar_spc>.segments.refined.txt This file contains the mapping between the RACA chromosome fragments and the genome sequences of the target species <tar_spc>. - ref_chrs.<out_spc>.segments.refined.txt This file contains the mapping between the RACA chromosome fragments and the genome sequences of the outgroup species <out_spc>. This file is created for each outgroup species. - rec_chrs.adjscores.txt This file constins the adjacency scores that were used to reconstruct the RACA chromosome fragments. Each column is defined as: Column1: the RACA chromosome fragment id Column2: start position (1-based) in the RACA chromosome fragment Column3: end position (1-based) in the RACA chromosome fragment Column4: the adjacency score - rec_chrs.size.txt This file contains the total size (the second column) and the total number of target scaffolds (the third column) that are placed in each RACA chromosome fragment (the first column). There are other intermediate files and directories in the output directory. They can be safely ignored. 4. How to ask questions? ------------------------ Contact Jaebum Kim ([email protected])
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.