CAGEscan clustering tools
Copyright: 2011-2013 RIKEN Omics Science Center 2013-2015 RIKEN Center for Life Science Technologies, Division of Genomics Technologies Author: Nicolas Bertin <email@example.com> License: GNU public license version 2 (GPL v2) This program is 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 2 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, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
This work was supported by a research grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) for the RIKEN Omics Science Center to Yoshihide Hayashizaki, and by a research grant from MEXT to the RIKEN Center for Life Science Technologies.
Create CAGEscan clusters from paired-end data in BED12, BAM or SAM format, using the data itself as a guide or an optional list of CAGE Tag Starting Site (CTSS) clusters in BED6 format.
CAGEscan-Clustering is a Perl script written at RIKEN, that calls
pairedBamToBed12 and other programs from the BEDTools suite. It is fully
documented in the file CAGEscan-Clustering.pod.
- Initial public release
- Added a new option
- Made more portable with regard to awk versions.
- Updated for backwards-incompatible changes in BEDTools 2.20.0.
;;as internal separator, to accomodate for the presence of single semicolons in the name field of SAM, BAM or BED12 input (in particular for workflows using TagDust 2).
- Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Plessy, Bertin, Takahashi, Simone et al., Nat Methods. 2010 Jul;7(7):528-34. http://dx.doi.org/10.1038/nmeth.1470
- Definition of Promotome–Transcriptome Architecture Using CAGEscan Bertin et al., 2012. Chapter 3 of "Tag-Based Next Generation Sequencing", Wiley-VCH Verlag GmbH & Co. KGaA http://dx.doi.org/10.1002/9783527644582.ch3
- Digital expression profiling of the compartmentalized translatome of Purkinje neurons. Kratz, Beguin et al., Genome Res. 2014 24:1396-1410. http://dx.doi.org/10.1101/gr.164095.113
- A Python implementation that does only distance clustering from BED12 input (no support for SAM/BAM input, nor external cluster definition).
- pairedBamToBed12, the tool that converts 'properly paired' BAM alignments to BED12 format, to ease the display and analysis of CAGEscan data.