Stringtie output gtf file only contains STRG,no original annotations

Question

[yiren]

Hi,

I am trying to generate novel genes transcripts expression following the stringtie manual. The stringtie --merge mode takes as input a list of all the assembled transcripts files (in GTF format) previously obtained for each sample, as well as a reference annotation file (-G option).The merged.gtf file geneid is STRG flag,but not the reference geneid,such as below.

chr1A_  StringTie   transcript  4059    4397    1000    +   .   gene_id "MSTRG.3"; transcript_id "C1_00010W_A-T"; ref_gene_id "C1_00010W_A"; 
chr1A   StringTie   exon    4059    4397    1000    +   .   gene_id "MSTRG.3"; transcript_id "C1_00010W_A-T"; exon_number "1"; ref_gene_id "C1_00010W_A"; 
chr1A   StringTie   transcript  4409    5266    1000    -   .   gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; 
chr1A   StringTie   exon    4409    4527    1000    -   .   gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1"; 
chr1A   StringTie   exon    4556    5266    1000    -   .   gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "2"; 
chr1A   StringTie   transcript  4409    4720    1000    -   .   gene_id "MSTRG.4"; transcript_id "C1_00020C_A-T"; ref_gene_id "C1_00020C_A"; 
chr1A   exon    4409    4720    1000    -   .   gene_id "MSTRG.4"; transcript_id "C1_00020C_A-T"; exon_number "1"; ref_gene_id "C1_00020C_A";

when I use Ballgown for differential expression,I get the the file ballgown.gtf ,the gene_id is also STRG flag not ref_gene_id.the file is below

chr1    StringTie   transcript  126521  126612  .   +   .   gene_id "MSTRG.71"; transcript_id "C1_00720W_A-T"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1    StringTie   exon    126521  126556  .   +   .   gene_id "MSTRG.71"; transcript_id "C1_00720W_A-T"; exon_number "1"; cov "0.0";
chr1    StringTie   exon    126577  126612  .   +   .   gene_id "MSTRG.71"; transcript_id "C1_00720W_A-T"; exon_number "2"; cov "0.0";
chr1    StringTie   transcript  204985  205057  .   +   .   gene_id "MSTRG.103"; transcript_id "C1_01020W_A-T"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1    StringTie   exon    204985  205057  .   +   .   gene_id "MSTRG.103"; transcript_id "C1_01020W_A-T"; exon_number "1"; cov "0.0";
chr1    CGD transcript  296046  296504  .   +   .   gene_id "C1_01500W_A"; transcript_id "C1_01500W_A-T"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";
chr1    CGD exon    296046  296504  .   +   .   gene_id "C1_01500W_A"; transcript_id "C1_01500W_A-T"; exon_number "1"; cov "0.0";

how can I get the file that geneid is ref_gene_id? help me for this thank you very much !!!

Answer 1

[MatthewP]

Hey, I recommend you check your input gtf file and annotation gtf/gff file, maybe your input gtf chromosome name is like chr1 style but your annotation file is 1 style.

[yiren]

thank you for you reply.input gtf file is same as annotation file .Some genes geneid are ref_gene_id,but almost genes geneid are STRG flag.