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. A CyVerse account (Register for a free CyVerse account at https://user.cyverse.org). 

  2. An up-to-date Java-enabled web browser.

Genome-guided mapping:

Input data requirements:

  1. Reference Genome (FASTA) or HISAT2 Indexed Reference Genome (in a subdirectory)
  2. Reference Transcriptome (GFF3/GTF/GFF)
  3. RNA-Seq reads (FASTQ) - Single end or Paired-end (compressed or uncompressed) or multiple NCBI SRA id's (each SRA ID on a separate row in the text file).

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  1. Index: This folder consists of the index of the genome
  2. Output: This folder consists of the output from HISAT2, Stringtie and Cuffcompare as well as the Feature_counts and FASTqc (optional) folders.
    1. In turn, this folder will consist of five files associated with each SRA or FASTq:
      1. A filtered GTF (if either the read/base or FPKM filter was set).
      2. A sorted.bam file of all mapped and unmapped reads.
      3. An index associated with the above BAM file.
      4. a GTF that represents the unprocessed file straight out of Stringtie if the user would like to investigate their data further.
      5. A combined.gtf that is the output of the cuffmerge step of RMTA (comparing all identified transcripts back to the reference to identify novel transcripts). This file is useful for novel transcript identification.
    2. The Feature_counts folder contains one file with all of the read count data for each gene across all SRA/FASTq files examined in the run.
    3. The FASTqc_out folder contains subfolders associated with each SRA/FASTq input file. In each folder is an html file with all of the details from the FASTqc run for each set of reads (1 for SE, 2 for PE).
  3. Logfiles: This folder consists of stout and sterr (information written to standard out or standard error log files) files as well as logs specific to running within the DE

 

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Transcriptome-guided Mapping:

  

Input data requirements:

 

  1. Reference Genome (FASTA) or HISAT2 Indexed Reference Genome (in a subdirectory)
  2. Reference Transcriptome (GFF3/GTF/GFF)
  3. RNA-Seq reads (FASTQ) - Single end or Paired-end (compressed or uncompressed) or multiple NCBI SRA id's (each SRA ID on a separate row in the text file).

 

  1. Mandatory fields

    1. Reference transcriptome

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    1. Input data
      Note

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

       

      1. 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
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          Note

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

      2. Single-end reads

        1. Single end FASTQ files or a HT path list of read files of single-end data
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      3. SRA

        1. Enter the SRA id, or
        2. Select a file containing a list of SRA ids (one per line) or a HT path list of multiple SRA ids list files
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    2. Parameters:

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    1.  

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    1.      i. Type of Sequence: Choose either Single End or Paired End

           ii. Choose RNA strandedness (default is unstranded)

           iii. Number of threads (Default is 4) 

           iv. Run FastQC

       
  
 
Example Runs:

The following test data using Arabidopsis are provided for testing RMTA in here - /iplant/home/shared/iplantcollaborative/example_data/RMTA (this path can be copied and pasted into the navigation bar in a data window within the DE)

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