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NameLongShortValueSinceDescription
COMPLETE3--cp3 Boolean2.2Require 3'-complete transcripts DEPRECATED, by (3.1) refactored to OUTOPTIONS.CP3
DIMENSION--dim-kInteger0.0

Dimension of the AS events to be extracted, Default is 2 (i.e. 'pairwise events'), and values < 2 stand for 'complete' events <TM>

EDGE_CONFIDENCE--ec Integer2.2

Level of confidence for edges (i.e., annotated transcription starts/poly-adenylation sites). The default is to trust no annotated edge and to extend overlapping first/last exons of a transcript to their most extreme position:

  • 0 if 'RefSeq' appears in the source field of the annotation
  • 1 if 'mRNA' appears in the source field of the annotation
  • 2 if 'EST' appears in the source field of the annotation
  • 3 if if none of the above applies

All transcript edges of confidence level > edgeConfidence are extended in case the annotation shows another exon with the same adjacent splice site and an earlier/later start/end.

EVENTS--events-e{ASE,ASI,DSP,VST}3.0

Types of events that are considered:

  • ASE: external AS events
  • ASI: internal AS events
  • DSP: adDitional SPlicing events
  • VST: Variable SiTe events
FLANK_TYPE--flankType Boolean2.2Output the type of the event flanks, i.e., 'constitutive' or 'alternative'. DEPRECATED, by (3.1) refactored to OUTOPTIONS.FTY
GENOME--genome-gFile2.2Path to a folder with genomic sequences, one per chromosome (.FASTA format). The header tags of each chromosome have to coincide with the <seqname> field ($1) of the annotation (GTF file).
GENEID_PARAM--gparam File3.1Name and path of a file with the GeneID models for splice sites
      
HELP -hBoolean3.0Help on usage, list of parameters and corresponding descriptions
INOPTIONS-io {CSS,IOK}3.1

Toggle criteria for elements of the input

  • CSS: consider canonical splice sites only
  • IOK: acceptable introns
INPUT--in-iFile0.0Input file with reference annotation (.GTF format), MANDATORY
INTRON_CONFIDENCE--ic Integer2.2

Level of intron confidence, below which introns are trusted without checks. The default is to trust all introns (i.e., ic= 255). Introns are assigned a confidency class:

  • 0 for 'RefSeq' appears in the source field of the annotation
  • 1 for 'mRNA' appears in the source field of the annotation
  • 2 for 'EST' appears in the source field of the annotation

All introns in transcripts of confidence level > threshold are discarded.

NMD--nmd  2.2Check nonsense-mediated decay conditions. DEPRECATED, by (3.1) refactored to OUTOPTIONS.NMD
OUTOPTIONS--oo {FLT,NMD,CP3}3.1

Flags to control output options for events:

  • CP3: predict 3'-complete
  • FLT: output flank type, i.e., 'constitutive' or 'alternative' site
  • NMD: predict NMD
  • SEQ: output splice site sequences
OUTPUT--out-oFile|stdout0.0Keyword 'stdout' for writing results to the standard output stream, or a fully qualified path to the output file. The parameter is optional--if nothing is specified, the output will be written to a file '<input file>_astalavista.gtf.gz'.
SEQ_SITE--seqsite Boolean2.2Output splice site sequences with events. DEPRECATED, by (3.1) refactored to OUTOPTIONS.SEQ
TMP_DIR--tmp File0.0The temporary directory, reads the environment variable when set to 'null'.
VARIANTS--vcf File3.1Name and path of a file with the variant information (.VCF format)
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