Filter flags

As the title suggests, these flags edit or remove content from the input file. Flag use depends on whether additional resources are provided such as fasta file or EnTAP annotation file.

• Basic flags
  • -p [prefix]
  • --false-run
  • --no-processing
  • --no-gene-redefining
  • --rem-3prime-incompletes
  • --rem-5prime-incompletes
  • --rem-5prime-3prime-incompletes
  • --rem-all-incompletes
  • --rem-monoexonics
  • --rem-multiexonics
  • --min-exon-size [number]
  • --min-intron-size [number]
  • --min-CDS-size [number]
  • --unique-genes-only
  • --sort-by-chromosome
• EnTAP required flags
  • --entap-annotation /path/to/your/final_annotation.tsv
  • --annotated-all-genes-only
  • --annotated-ss-genes-only
• Fasta required flags
  • --fasta /path/to/your/nucleotide/fasta.fasta
  • --canonical-only
  • --rem-genes-without-start-codon
  • --allow-alternate-starts
  • --rem-genes-without-stop-codon
  • --rem-genes-without-start-and-stop-codon
  • --allowed-inframe-stop-codons [number]
  • --splice-table
  • --nt-content