Menu
▾
▴
Tree [9b7c5a] master / History
Chaolin Zhang
Jie Wu
Read Me
OLego -- short or long RNA-seq read mapping to discover exon junction Jie Wu (wuj@cshl.edu), Chaolin Zhang (cz2294@columbia.edu) Please find the most recent documentation at http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation What is OLego? ====================== OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by strategic searches with very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow for fast processing of large-scale data. OLego is an open source code project and released under GPLv3. The implementation of OLego relies heavily on BWA (version 0.5.9rc1, http://bio-bwa.sourceforge.net/). Citation ====================== Wu,J., Anczukow,O., Krainer,A.R., Zhang,M.Q. , Zhang,C. , 2013. OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res. , In press. Versions ====================== v1.1.5 ( 7-14-2014 ) --------------------- * Bugs fixed * Optmization for speed v1.1.2 ( 7-1-2013 ) --------------------- * Sensitivity improved in small exons and single anchor search.by allowing mismatch. * Allows overlapping seeds to improve speed and seeding flexibility. * Increase default seed size to 15 (max 1 nt overlapping ) to keep both senstivity and speed. * A bug fixed (crashes when using -M 0 ) v1.1.1 ( 4-14-2013 ) --------------------- * Improved speed by filtering simple repetitive anchors. * Default options optimized. v1.1.0 ( 3-31-2013 ) --------------------- * Bug fixed for duplicate entries for some reads, sensitivity improved. * Optimized on option -W. * Bug fixed in sam2bed.pl. * Bug fixed for option -e. * Bug fixed for regression_model_gen. * Add support for gzip input file for sam2bed.pl. v1.0.8 ( 11-20-2012 ) --------------------- * Improvement in hit clustering. * Fixed an overcounting problem in mismatch counting. * Fixed bug in merging step. * Fixed bug in XS tag for extra exon body reads. * Allows pipe input/output with "-" for some of the scripts. v1.0.6 ( 08-09-2012 ) --------------------- * Added option --max-multi (default:1000) to avoid huge data in a single line. * Added option --num-reads-batch. * Fixed a bug in the junction connecting step. v1.0.5 ( 07-16-2012 ) --------------------- * Minor bug fixed (the old code crashes in a very rare case). v1.0.4 ( 06-12-2012 ) --------------------- * Option changes ( do single-anchor search by default now ). v1.0.3 ( 06-10-2012 ) --------------------- * Now supports strand specific library * Fixed bugs about XS v1.0.0 ( 05-15-2012 ) ---------------------- * The initial Public release
