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  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Basic options Input/Outputs 
    1. Transcript file in (s) in FASTA format (Mandatory)
    2. Reference genome containing all chromosomes/scaffolds in FASTA format (preferably with *.fasta, *.fa, *.fna, *.ffn or *.frn extension) OR 
      *.txt file containing the one-per-line list of FASTA files with reference sequences (Mandatory)
    3. GTF/GFF gene database file (needs information about parent relations). We recommend to use files downloaded from GENCODE or Ensembl (Optional)
    4. File with forward paired-end reads in FASTQ format.
    5. File with reverse paired-end reads in FASTQ format.
    6. File with single reads in FASTQ format
    7. Output directory to store all results.
    Advanced options
    1. .
  3. Options
    1.  Run with BLAT alignment tool instead of GMAP.
    2.  Run with TopHat tool instead of STAR for analyzing database coverage by reads.
    3. Name(s) of assemblies that will be used in the reports separated by space and given in the same order as files with transcripts / alignments. 
    4. Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand.
    5.  Do not draw plots (makes rnaQUAST run a bit faster).
    6.  Run with BLAT alignment tool instead of GMAP.
    7.  Run with TopHat tool instead of STAR for analyzing database coverage by reads.
    8.  Run with GeneMarkS-T gene prediction tool. 
    9. Run disable_infer_genes option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time.
    10. Run disable_infer_transcripts if your GTF file already contains transcripts records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time.

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