URL: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
Proper Citation: Cufflinks (RRID:SCR_014597)
Description: Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
Resource Type: software resource, data analysis software, sequence analysis software, data processing software, software application
Defining Citation: DOI:10.1038/nbt.1621
Keywords: transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools
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