Entering edit mode
6.3 years ago
blooming.daisy333
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110
hi,
i have used stringtie for the transcript assembly. stringtie is assigning its own labels (i.e gene IDs and transcript IDs) whle I need original gene IDs. can someone kindly suggest the way to get original IDs for the assembed transcripts from genome annotation file?? the stringtie output and genome annotation look like this:
stringtie output file:;
chr1 StringTie transcript 328661 330868 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1";
chr1 StringTie exon 328661 329729 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1";
chr1 StringTie exon 329840 330067 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "2";
chr1 StringTie exon 330758 330868 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "3";
chr1 StringTie transcript 580963 583751 1000 - . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1";
chr1 StringTie exon 580963 582109 1000 - . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1";
chr1 StringTie exon 583479 583751 1000 - . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "2";
genome annotation file
chr4 GLEAN mRNA 123284514 123288477 0.999991 - . ID=Cotton_A_18927_BGI-A2_v1.0;Name=Cotton_A_18927;source_id=CottonA_GLEAN_10022228;identical_support_id=CUFF67.1103.1;evid_id=Cot030308.1
chr4 GLEAN CDS 123288376 123288477 . - 0 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123287662 123287826 . - 0 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123287427 123287536 . - 0 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123287129 123287237 . - 1 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123286939 123287051 . - 0 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123286180 123286330 . - 1 Parent=Cotton_A_18927_BGI-A2_v1.0
chr4 GLEAN CDS 123284514 123285671 . - 0 Parent=Cotton_A_18927_BGI-A2_v1.0
chr9 GLEAN mRNA 17802711 17803334 1 + . ID=Cotton_A_16149_BGI-A2_v1.0;Name=Cotton_A_16149;source_id=CottonA_GLEAN_10030787;evid_id=Cot023903.1
chr9 GLEAN CDS 17803146 17803334 . + 0 Parent=Cotton_A_16149_BGI-A2_v1.0
chr9 GLEAN CDS 17802984 17803035 . + 1 Parent=Cotton_A_16149_BGI-A2_v1.0
chr9 GLEAN CDS 17802711 17802862 . + 0 Parent=Cotton_A_16149_BGI-A2_v1.0
thanks in anticipation
Can you please upload the StringTie syntax?
yes please
stringtie <aligned_reads.bam> [options]*
and here is its manual
http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
may i know the answer for the above query