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Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq.
Instruction for installation and usage can be found here.
A full example pipeline to go from RNA-Seq reads to differential gene expression results on non-model organisms is also provided here.
Questions should be posted to our google group
Authors: Nadia M. Davidson and Alicia Oshlack
October 26th 2016: Want to load your de novo assembled clusters into IGV and visualise read coverage? or find differential transcript usage? Check out our new method Lace and find out about superTranscripts.
April 1st 2016: New version of corset released corset version 1.05
May 5th 2015: Because google code is shutting down, we've moved out webpage to gitHub. The google group will remain where it is.
July 26th 2014: Our paper is now out at Genome Biology
July 11th 2014: We are finally ready to release corset version 1.00! This version has some major improvements to the amount of memory used and some minor improvements for speed. Please keep giving feedback on the google group.