The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Cufflinks – Transcript Quantification and Assembly

Cufflinks (http:/cufflinks.cbcb.umd.edu/) assembles transcripts from RNA-Seq data, estimates their abundances, and tests for differential expression and regulation.

  • To use Cufflinks, either upload your own BAM or SAM file or perform an alignment using TopHat, BOWTIE, SOAP, or BWA and use the resulting BAM file.
  • Resources: documentation

Community Data > iplantcollaborative > example_data > cufflinks_transcript_quantification_and_assembly

  • Use SRR070570_WT.fastq.tophat.bam (539 MB) as a test input file.

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Use these parameters within the DE app interface:
    • Select Reference Genome Annotation - Arabidopsis thaliana (Ensembl 14)
    • Prefix for transcripts in reported GTF - WT
    • All other parameters should remain at their default values
  • Expect three files as output: genes.fpkm_tracking, isoforms.fpkm_tracking, and transcripts.gtf. The fpkm_tracking files contain quantitative columns that indicate the expression level for each transcript, while transcripts.gtf contains the reconstructed transcripts based on the RNAseq data.