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5.9 years ago
blooming.daisy333
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110
hi all,
for my project I need to determine and classify the alternate splicing (AS) events. I have used ASTALAVASTA software for this purpose that has successfully determined the AS events with code for the gtf annotation input file generated by stringtie. the problem is that it is not providing me any information about the classification of these events like whetehr they are exon skipping, intron retension, alternative doner or alterntive acceptors. it provides codes only for these 5 classes but my results contain large variety of other types (mixed, have transcription start/end or novel for which it provide no info). I have tried to group the one that have mixed anatomy in these 5 classes but it is pretty confusing. can anyone help me how could i classify these events???
or may suggest any other good tool for this purpose plz.
kind help would be highly appreciated.
my output file of ASTALAVASTA looks like this:
chr1 Undefined as_event 581052 581358 . + . transcript_id "STRG.5.2,STRG.5.1"; gene_id "chr1:581052-583794W"; flanks "581052[,581358-"; structure "1^,2^"; splice_chain "581257^,581276^"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 581052 582101 . + . transcript_id "STRG.5.3,STRG.5.2"; gene_id "chr1:581052-583794W"; flanks "581052[,582101]"; structure "0,1^2-"; splice_chain ",581257^581358-"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 581052 583794 . + . transcript_id "STRG.5.1,STRG.5.3"; gene_id "chr1:581052-583794W"; flanks "581052[,null"; structure "1^2-4^5-6],3]"; splice_chain "581276^581358-582109^583479-583794],582101]"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_3";
chr1 Undefined as_event 950006 957972 . + . transcript_id "STRG.34.1,STRG.35.1"; gene_id "chr1:950006-957972W"; flanks "null,null"; structure "1[2^7-8],3[4^5-6]"; splice_chain "950006[950090^957762-957972],950774[950968^951662-952237]"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 974385 976220 . + . transcript_id "STRG.40.1,STRG.40.2"; gene_id "chr1:973650-976220W"; flanks "974385[,976220]"; structure "1^2-4^6-,3^5-"; splice_chain "975147^975385-975564^975721-,975477^975634-"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 973650 976220 . + . transcript_id "STRG.40.3,STRG.40.1"; gene_id "chr1:973650-976220W"; flanks "null,null"; structure "1[7],2[3^4-5^6-8]"; splice_chain "973650[975869],974385[975147^975385-975564^975721-976220]"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_3";
chr1 Undefined as_event 973650 976220 . + . transcript_id "STRG.40.3,STRG.40.2"; gene_id "chr1:973650-976220W"; flanks "null,null"; structure "1[5],2[3^4-6]"; splice_chain "973650[975869],974385[975477^975634-976220]"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_3";
chr1 Undefined as_event 1297130 1298623 . + . transcript_id "STRG.53.1,STRG.53.2"; gene_id "chr1:1297130-1298623W"; flanks "1297130[,null"; structure "1^3-4],2]"; splice_chain "1298245^1298432-1298623],1298254]"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 1646433 1647884 . + . transcript_id "STRG.70.1,STRG.70.2"; gene_id "chr1:1646433-1647884W"; flanks "null,1647884]"; structure "1[2^4-,3["; splice_chain "1646433[1646513^1646837-,1646754["; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
chr1 Undefined as_event 1869897 1870747 . + . transcript_id "STRG.79.1/STRG.79.3,STRG.79.2"; gene_id "chr1:1868804-1873243W"; flanks "1869897^,1870747^"; structure "1-,2-"; splice_chain "1870664-,1870669-"; sources "Undefined,Undefined"; NMorMRNA "null"; degree "4"; dimension "2_2";
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";
