SUMMARY: We present 'Threshold-seq,' a new approach for determining thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset before it can be considered different from 'background.' The proposed scheme is easy to implement and incorporate into existing pipelines. AVAILABILITY AND IMPLEMENTATION: Source code of Threshold-seq is freely available as an R package at: http://cm.jefferson.edu/threshold-seq/. CONTACT: isidore.rigoutsos@jefferson.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: We present 'Threshold-seq,' a new approach for determining thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset before it can be considered different from 'background.' The proposed scheme is easy to implement and incorporate into existing pipelines. AVAILABILITY AND IMPLEMENTATION: Source code of Threshold-seq is freely available as an R package at: http://cm.jefferson.edu/threshold-seq/. CONTACT: isidore.rigoutsos@jefferson.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Eric Londin; Phillipe Loher; Aristeidis G Telonis; Kevin Quann; Peter Clark; Yi Jing; Eleftheria Hatzimichael; Yohei Kirino; Shozo Honda; Michelle Lally; Bharat Ramratnam; Clay E S Comstock; Karen E Knudsen; Leonard Gomella; George L Spaeth; Lisa Hark; L Jay Katz; Agnieszka Witkiewicz; Abdolmohamad Rostami; Sergio A Jimenez; Michael A Hollingsworth; Jen Jen Yeh; Chad A Shaw; Steven E McKenzie; Paul Bray; Peter T Nelson; Simona Zupo; Katrien Van Roosbroeck; Michael J Keating; George A Calin; Charles Yeo; Masaya Jimbo; Joseph Cozzitorto; Jonathan R Brody; Kathleen Delgrosso; John S Mattick; Paolo Fortina; Isidore Rigoutsos Journal: Proc Natl Acad Sci U S A Date: 2015-02-23 Impact factor: 11.205
Authors: Nicole Cloonan; Shivangi Wani; Qinying Xu; Jian Gu; Kristi Lea; Sheila Heater; Catalin Barbacioru; Anita L Steptoe; Hilary C Martin; Ehsan Nourbakhsh; Keerthana Krishnan; Brooke Gardiner; Xiaohui Wang; Katia Nones; Jason A Steen; Nicholas A Matigian; David L Wood; Karin S Kassahn; Nic Waddell; Jill Shepherd; Clarence Lee; Jeff Ichikawa; Kevin McKernan; Kelli Bramlett; Scott Kuersten; Sean M Grimmond Journal: Genome Biol Date: 2011-12-30 Impact factor: 13.583
Authors: Tuuli Lappalainen; Michael Sammeth; Marc R Friedländer; Peter A C 't Hoen; Jean Monlong; Manuel A Rivas; Mar Gonzàlez-Porta; Natalja Kurbatova; Thasso Griebel; Pedro G Ferreira; Matthias Barann; Thomas Wieland; Liliana Greger; Maarten van Iterson; Jonas Almlöf; Paolo Ribeca; Irina Pulyakhina; Daniela Esser; Thomas Giger; Andrew Tikhonov; Marc Sultan; Gabrielle Bertier; Daniel G MacArthur; Monkol Lek; Esther Lizano; Henk P J Buermans; Ismael Padioleau; Thomas Schwarzmayr; Olof Karlberg; Halit Ongen; Helena Kilpinen; Sergi Beltran; Marta Gut; Katja Kahlem; Vyacheslav Amstislavskiy; Oliver Stegle; Matti Pirinen; Stephen B Montgomery; Peter Donnelly; Mark I McCarthy; Paul Flicek; Tim M Strom; Hans Lehrach; Stefan Schreiber; Ralf Sudbrak; Angel Carracedo; Stylianos E Antonarakis; Robert Häsler; Ann-Christine Syvänen; Gert-Jan van Ommen; Alvis Brazma; Thomas Meitinger; Philip Rosenstiel; Roderic Guigó; Ivo G Gut; Xavier Estivill; Emmanouil T Dermitzakis Journal: Nature Date: 2013-09-15 Impact factor: 49.962
Authors: Eric Londin; Rogan Magee; Carol L Shields; Sara E Lally; Takami Sato; Isidore Rigoutsos Journal: Pigment Cell Melanoma Res Date: 2019-08-16 Impact factor: 4.693
Authors: Sinisa Simonovic; Christian Hinze; Kai M Schmidt-Ott; Jonas Busch; Monika Jung; Klaus Jung; Anja Rabien Journal: BMC Urol Date: 2020-02-04 Impact factor: 2.264