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NameTool(s)LongShortValueSinceDescription
COMPLETE3asta--cp3 Boolean2.2Require 3'-complete transcripts DEPRECATED, by (3.1) refactored to OUTOPTIONS.CP3

GENOME

CHR_SEQ

all

--genome

--chr

-g

-c

File

2.2

3.1

Path 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).
EVENTSasta--ev-e{ASE,ASI,DSP,VST}3.1

Types of events that are considered:

  • ASE: external AS events
  • ASI: internal AS events
  • DSP: adDitional SPlicing events
  • VST: Variable SiTe events
EVENTS_ATRasta--ea-a{CP3,CSS,FLT,IOK,NMD,SEQ}3.1

Event Attributes

  • CP3: predict 3'-complete
  • CSS: consider only introns with canonical splice sites
  • FLT: output flank type, 'constitutive' or 'alternative'
  • IOK: consider only introns that are acceptable considering basic splicing rules
  • NMD: predict NMD
  • SEQ: output splice site sequences of event flanks
EVENTS_DIMENSIONasta

 

--ed

-k

-d

Integer

0.0

3.1

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

EVENTS_FILEasta

--out

--eo

-oFile|stdout

0.0

3.1

Keyword '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'.
EVENTS_OPTasta--ep-p{FLT,NMD,CP3}3.1

Flags to control output options for events:

  • CP3: predict 3'-complete
  • CSS: consider canonical splice sites only
  • FLT: output flank type, i.e., 'constitutive' or 'alternative' site
  • IOK: acceptable introns
  • NMD: predict NMD
  • SEQ: output splice site sequences
EDGE_CONFIDENCEasta--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.

DEPRECATED, to be refactored (soon)

FLANK_TYPEasta--flankType Boolean2.2Output the type of the event flanks, i.e., 'constitutive' or 'alternative'. DEPRECATED, by (3.1) refactored to OUTOPTIONS.FTY
GENE_IDscorer--gid-gFile3.1Name and path of the GeneID parameter file with models for splice sites
HELPall -hBoolean3.0Help on usage, list of parameters and corresponding descriptions

INPUT

IN_FILE

all--in-iFile

0.0

3.1

Input file with reference annotation (.GTF format), MANDATORY
INTRON_CONFIDENCEasta--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.

DEPRECATED, to be refactored (soon)

NMDasta--nmd  2.2Check nonsense-mediated decay conditions. DEPRECATED, by (3.1) refactored to OUTOPTIONS.NMD
SITESscorer--ss-s{SSD,SSA,TSS,CLV,SST,SND,AUG,STP}3.1

Types of sites that are output:

  • SSD: Splice Site Donor
  • SSA: Splice Site Acceptor
  • TSS: Transcription Start Site
  • CLV: Cleavage Site
  • SST: Soft Start (Unconfirmed 5'-end of transcribed sequence)
  • SND: Soft End (Unconfirmed 3'-end of transcribed sequence)
  • AUG: Start Codon
  • STP: Stop Codon
SITE_FILEscorer--so-fFile|stdout3.1Keyword 'stdout' for writing results to the standard output stream, or a fully qualified path to the output file.
SITE_OPTasta--sp-t{SSS}3.1

Flags to control optional output for sites:

  • SSS: Splice Site Score
SEQ_SITEasta--seqsite Boolean2.2Output splice site sequences with events. DEPRECATED, by (3.1) refactored to EVENTS_ATR
TMP_DIRall--tmp File0.0The temporary directory, reads the environment variable when set to 'null'.
VARIANT_FILEscorer--vcfvFile3.1Name and path of a file with the variant information (.VCF format)
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