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HELP

Toggle criteria for elements of the input

  • CSS: consider canonical splice sites only
    • IOK: acceptable introns
    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

    		EVENT_DIMENSION--dim-k

    		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

    GENOME

    CHROMOSOMEGENE_SEQID    		--genomescorer--chrgid-g

    -c

    		File2.23.1Path 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).GENE_ID--gid File3.1Name 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), MANDATORYIN_OPTIONS-io {CSS,IOK}3.1
    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
    OUT_EVENTS--oev-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
    OUT_EVENTS_OPT--oeo-v{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' siteNMD: predict NMD
  • SEQ: output splice site sequences
  • IOK: acceptable introns
    		• OUT_FILE--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'.
    OUT_FILE_SITES--ous-pFile|stdout3.1Keyword 'stdout' for writing results to the standard output stream, or a fully qualified path to the output file.scorer--ssOUT_SITES--ost-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--spOUT_SITES_OPT--oso-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 OUTOPTIONS.SEQEVENTS_ATR
    TMP_DIRall--tmp File0.0The temporary directory, reads the environment variable when set to 'null'.
    VARIANT_FILEscorer--vcf vFile3.1Name and path of a file with the variant information (.VCF format)