Cufflinks Software Suite Tuxedo. 70 years ago by. Bowtie Version in GenePattern public repository.
The RNA-seq pipeline Tuxedo consists of the TopHat spliced read mapper that internally uses Bowtie or Bowtie 2 short read aligners and several Cufflinks tools that allows one to assemble transcripts estimate their abundances and tests for differential expression and regulation in RNA-Seq samples. The transcriptsgtf file is one of the inputs to cuffdiff. Cufflinks 221 released May 05 2014.
The Tuxedo suite offers a set of tools for analyzing a variety of RNA-Seq data including short-read mapping identification of splice junctions transcript and isoform detection differential expression visualizations and quality control metrics.
ADD COMMENT link written 71 years ago by gleparc 470. Cufflinks is a part of the Tuxedo suite. The transcriptsgtf file is one of the inputs to cuffdiff. Bowtie Version in GenePattern public repository.