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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  1. Mandatory fields

    1. Analysis Name

      1. Choose an appropriate name for your analysis and make comments if you wish. Default name is shown in the figure below.

      2. Select the output folder for the results of the analysis.

    2. Genome guided mapping


      ***Select at least one of the below two options for the indexing of the Reference Genome***

      1. Custom genome (required)
      2. HISAT2 Indexed folder (for indexed genomes)

        Image Modified

    3. Select an aligner


      ***Only one of the below two options needs to be selected. Both cannot be selected.***

      i) Hisat2
      ii) Bowtie2

      titleWhen to use HISAT2 or Bowtie2

      HISAT2 is a splice-aware algorithm used to perform reference genome-based read mapping. Stringtie is then used to assemble transcripts based on this read mapping.

      The read aligner Bowtie2 has been included as an optional aligner in the RMTA workflow for users wishing to call single nucleotide polymorphisms (SNPs) from their RNA-seq (or DNA-seq) data in a high throughput manner. When the Bowtie2 option is selected, HISAT2 and Stringtie are both removed from the workflow, but the additional option to remove duplicate reads (important for population level analyses) becomes available.

    4. Reference annotation


      ***Providing reference annotation is optional and not required when doing de novo transcriptome assembly***

    5. Featurecount optionsFeature Count Options
      1. Choose a Feature Type. The default option will be "exon"
      2. Choose a Gene Attribute. The default option will be "gene_id"
      3. Select the Type of Strandedness. The three options include unstranded, stranded, and reversely stranded.
      4. Please refer to your Genome Annotation File (.gtf), and confirm that these settings match your data. For Gene Attribute, be sure that gene_id is written before the name of each gene.

    6. Input reads



      ***Only one of the following three read options (d, e, or f) may be selected per job.***


      Paired-end reads

      1. FASTQ Files (Read 1): HT path list of read 1 files of paired-end data
      2. FASTQ Files (Read 2): HT path list of read 2 files of paired-end data



      ***When inserting multiple paired end FASTQ files, be sure that reads 1 and 2 have matching patterns***