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- A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Basic options Input/Outputs
- Transcript file in (s) in FASTA format (Mandatory)
- 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) - GTF/GFF gene database file (needs information about parent relations). We recommend to use files downloaded from GENCODE or Ensembl (Optional)
- File with forward paired-end reads in FASTQ format.
- File with reverse paired-end reads in FASTQ format.
- File with single reads in FASTQ format
- Output directory to store all results.
- .
- Options
- Run with BLAT alignment tool instead of GMAP.
- Run with TopHat tool instead of STAR for analyzing database coverage by reads.
- 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.
- 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.
- Do not draw plots (makes rnaQUAST run a bit faster).
- Run with BLAT alignment tool instead of GMAP.
- Run with TopHat tool instead of STAR for analyzing database coverage by reads.
- Run with GeneMarkS-T gene prediction tool.
- 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.
- 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.
- Run with BLAT alignment tool instead of GMAP.
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