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README.md

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 <nbertin@gsc.riken.jp>
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.

CAGEscan-Clustering

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.

Release history

Version 1.0

  • Initial public release

Version 1.1

  • Added a new option fit_to_guiding_cluster_size.
  • Made more portable with regard to awk versions.
  • Updated for backwards-incompatible changes in BEDTools 2.20.0.

Version 1.2

  • Use ;; 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).

See also

About

Create CAGEscan clusters from CAGE paired-end reads

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