The AStalavista tool asta extracts all alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, AStalavista detects the variations in their splicing structure and identify all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase,...The output is provided in a specific GTF format.



Pairwise AS event extraction from a transcriptome
astalavista -t asta -i <annotation.gtf>

where <annotation.gtf> is an annotation in GTF format. The output file (also a GTF format for AS events) is written to the same folder as the input, and can be redirected by the command line flag "–eo". For more information, cf. the Section Parameters.

Complete AS events
astalavista -t asta -i <annotation.gtf> -d 0

The command retrieves events in their complete resolution according to the provided transcriptome annotation <annotation.gtf>: events with two, three, four, etc. alternate variants are output together instead of breaking them down to pairwise events.

Including events linked to alternative transcription initiation and alternative poly-adenylation, cleavage and 3'-end formation
astalavista -t asta -i <annotation.gtf> -e [ASE,ASI]

The command line flag "-e" specifies the types of events that are collected: ASE are "external" AS events that include splicing variations linked to alternative transcription start and polyA/cleavage sites, ASI are "internal" AS events that are delimited by common splice sites at both ends. More information about different event type options can be found in the Section Parameters.

Outputting splice site sequences
astalavista -t asta -i <annotation.gtf> -c <genome-folder> -a [SEQ]	

Output splice sites with their flanking splice site sequences. (warning) Note that for obtaining sequences, FASTA files with the genomic sequence are required (e.g. chr1.fasta, chr2.fasta, scaffoldXYZ.fasta, ...).

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