Hi all,

I built a new annotation file out of long reads data with StringTie. When I opened the resulting GTF file, I noticed that all features except exons and transcripts disappeared. So we lose all the data on 5' or 3'UTR, CDS, start and stop codons.

I wonder if merging them would be a good idea to recover this type of data (at least for the genes that have not been modified by StringTie). Do you know of any tool that could do that ? I tried to merge them with cuffmerge and gffcompare. None of the two give the results that I would expect (a merged file with data on exons, CDS, UTR...).

Here is a sample of the reference file I used (where there was data on UTR, CDS...):

> cat ref_olig2.gtf
chr1    ncbiRefSeq  transcript  106522741   106524545   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1";  gene_name "OLIG2";
chr1    ncbiRefSeq  exon    106522741   106522781   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "1"; exon_id "NM_001031526.1.1"; gene_name "OLIG2";
chr1    ncbiRefSeq  5UTR    106522741   106522781   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "1"; exon_id "NM_001031526.1.1"; gene_name "OLIG2";
chr1    ncbiRefSeq  exon    106523018   106524545   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";
chr1    ncbiRefSeq  5UTR    106523018   106523036   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";
chr1    ncbiRefSeq  CDS 106523037   106523930   .   +   0   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";
chr1    ncbiRefSeq  3UTR    106523934   106524545   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";
chr1    ncbiRefSeq  start_codon 106523037   106523039   .   +   0   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";
chr1    ncbiRefSeq  stop_codon  106523931   106523933   .   +   0   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; exon_id "NM_001031526.1.2"; gene_name "OLIG2";

Here is the same region in the new GTF (to make it simple, I chose a region that has not been modified by StringTie):

> cat stringtie_olig2.gtf
chr1    ncbiRefSeq  transcript  106522741   106524545   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; gene_name "OLIG2"; ref_gene_id "OLIG2";
chr1    ncbiRefSeq  exon    106522741   106522781   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "1"; gene_name "OLIG2";
chr1    ncbiRefSeq  exon    106523018   106524545   .   +   .   gene_id "OLIG2"; transcript_id "NM_001031526.1"; exon_number "2"; gene_name "OLIG2";

Result of gffcompare (only transcript and exons):

> gffcompare stringtie_olig2.gtf ref_olig2.gtf
> cat gffcmp.combined.gtf
chr1    ncbiRefSeq  transcript  106522741   106524545   .   +   .   transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; gene_name "OLIG2"; oId "NM_001031526.1"; tss_id "TSS1";
chr1    ncbiRefSeq  exon    106522741   106522781   .   +   .   transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "1";
chr1    ncbiRefSeq  exon    106523018   106524545   .   +   .   transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "2";

Result of cuffmerge (only exons):

> cuffmerge -g ref.olig2.gtf list_cuffmerge.txt
> cat list_cuffmerge.txt
stringtie_olig2.gtf 
> cat merged_asm/merged.gtf
    chr1    Cufflinks   exon    106522741   106522781   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "OLIG2"; oId "NM_001031526.1"; nearest_ref "NM_001031526.1"; class_code "="; tss_id "TSS1";
    chr1    Cufflinks   exon    106523018   106524545   .   +   .   gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "OLIG2"; oId "NM_001031526.1"; nearest_ref "NM_001031526.1"; class_code "="; tss_id "TSS1";