hi all,
i ve used ASTALAVASTA software to determine alternate splicing events and have following output:
chr1 Undefined as_event 1871874 1873243 . + . transcript_id "STRG.79.1/STRG.79.2,STRG.79.3" gene_id "chr1:1868804-1873243W" flanks "1871874-,null" structure "1^3-4],2]" splice_chain "1872150^1873095-1873243],1872197]" sources "Undefined,Undefined" NMorMRNA "null" degree "4" dimension "2_2"
chr1 Undefined as_event 1886878 1887691 . + . transcript_id "STRG.81.1,STRG.81.2" gene_id "chr1:1884860-1891139W" flanks "1886878^,1887691^" structure "1-,2-" splice_chain "1887614-,1887619-" sources "Undefined,Undefined" NMorMRNA "null" degree "4" dimension "2_2"
chr1 Undefined as_event 2119498 2121140 . + . transcript_id "STRG.98.1,STRG.98.2" gene_id "chr1:2118059-2121140W" flanks "2119498-,null" structure "1^3-4^5-6],2]" splice_chain "2119561^2119968-2120288^2120951-2121140],2119570]" sources "Undefined,Undefined" NMorMRNA "null" degree "4" dimension "2_2"
chr1 Undefined as_event 2381238 2381766 . + . transcript_id "STRG.120.2,STRG.120.1" gene_id "chr1:2380953-2383475W" flanks "2381238^,2381766-" structure "0,1-2^" splice_chain ",2381490-2381595^" sources "Undefined,Undefined" NMorMRNA "null" degree "4" dimension "2_2"
my question is that it is easy to classify the result of second and fourth line however i could ot understand what does it mean of the [ ] in the following results "1^3-4^5-6],2]" and "1^3-4],2]" and how they are classified???
waiting for the kind help
many thanks
•
written
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blooming.daisy333 •
Splicing sites can be of the following types: 1 Acceptor site (symbol: -); 2 Donor site (symbol:^); 3 Transcription start site (symbol: [); 4 Transcription end site (symbol:]). Excerpt from R package: SplicingGraphs manual pdf
thanks for the kind help.
can you plz send me the link. im unable to find it....
sorry I can't add reply directly，maybe caused by my network. Here is the link: http://www.bioconductor.org/packages/release/bioc/html/SplicingGraphs.html Please check the Reference Manual PDF .
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