Hi All.
I am using StringTie to assemble transcriptome from my RNA-Seq data. The question is that if I use refSeq as reference annotation which was download from UCSC genome browser website, does the CDS, start codon and stop codon segments in that gtf file will affect transcriptome assembly? Like would StringTie consider CDS/start codon/stop codon as a new exon, but actually these features are just parts of exons?

The gtf file looks like this:

chr1	hg19_refGene	start_codon	67000042	67000044	0.000000	+	.	gene_id "NM_032291"; transcript_id "NM_032291"; 

chr1	hg19_refGene	CDS	67000042	67000051	0.000000	+	0	gene_id "NM_032291"; transcript_id "NM_032291"; 

chr1	hg19_refGene	exon	66999639	67000051	0.000000	+	.	gene_id "NM_032291"; transcript_id "NM_032291"; 

chr1	hg19_refGene	CDS	67091530	67091593	0.000000	+	2	gene_id "NM_032291"; transcript_id "NM_032291"; 

chr1	hg19_refGene	exon	67091530	67091593	0.000000	+	.	gene_id "NM_032291"; transcript_id "NM_032291"; 
hi,
Plz. do not use this GTF file from UCSC. A GTF file not only has the information of individual exons (of a transcript isoform) but also of different transcripts (that originate from a particular gene).
You would notice that the `gene_id` and `transcript_id` are same in the above GTF file. So any transcript assembler you use (like StringTie) would not be able to infer the transcript <-> gene relationship.

See this GTF structure from Ensembl -

    1	protein_coding	exon	874655	874840	.	+	.	gene_id "ENSG00000187634"; transcript_id "ENST00000455979"; exon_number "1"; gene_name "SAMD11"; gene_biotype "protein_coding"; transcript_name "SAMD11-004"; exon_id "ENSE00002715021";
    1	protein_coding	CDS	874655	874840	.	+	2	gene_id "ENSG00000187634"; transcript_id "ENST00000455979"; exon_number "1"; gene_name "SAMD11"; gene_biotype "protein_coding"; transcript_name "SAMD11-004"; protein_id "ENSP00000412228";
    1	protein_coding	exon	876524	876686	.	+	.	gene_id "ENSG00000187634"; transcript_id "ENST00000455979"; exon_number "2"; gene_name "SAMD11"; gene_biotype "protein_coding"; transcript_name "SAMD11-004"; exon_id "ENSE00003477353";
    1	protein_coding	CDS	876524	876686	.	+	2	gene_id "ENSG00000187634"; transcript_id "ENST00000455979"; exon_number "2"; gene_name "SAMD11"; gene_biotype "protein_coding"; transcript_name "SAMD11-004"; protein_id "ENSP00000412228";

Hope this is clear. Plz use GTF from [Ensembl][1] or [Gencode][2]


  [1]: ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/
  [2]: http://www.gencodegenes.org/releases/current.html