exons with same transcirpt_id

31 views
Skip to first unread message

Grant

unread,
Nov 23, 2017, 10:57:47 AM11/23/17
to rna-star
Dear Alex,

My gtf file (which I got by converting gff file using gffread) has this kind of information:

ctro_c_1    CGOB    exon    27749    28666    .    +    .    transcript_id "ctro_CGOB_00001_mRNA"; gene_id "ctro_CGOB_00001"; gene_name "ctro_CGOB_00001";
ctro_c_1    CGOB    CDS    27749    28666    .    +    0    transcript_id "ctro_CGOB_00001_mRNA"; gene_id "ctro_CGOB_00001"; gene_name "ctro_CGOB_00001";
ctro_c_1    CGOB    exon    770839    771455    .    -    .    transcript_id "ctro_CGOB_00002_mRNA"; gene_id "ctro_CGOB_00002"; gene_name "ctro_CGOB_00002";
ctro_c_1    CGOB    exon    771521    771554    .    -    .    transcript_id "ctro_CGOB_00002_mRNA"; gene_id "ctro_CGOB_00002"; gene_name "ctro_CGOB_00002";
ctro_c_1    CGOB    CDS    770839    771455    .    -    2    transcript_id "ctro_CGOB_00002_mRNA"; gene_id "ctro_CGOB_00002"; gene_name "ctro_CGOB_00002";
ctro_c_1    CGOB    CDS    771521    771554    .    -    0    transcript_id "ctro_CGOB_00002_mRNA"; gene_id "ctro_CGOB_00002"; gene_name "ctro_CGOB_00002";


ctro_CGOB_00002 has two exons but both have the same transcript_id  ctro_CGOB_00002_mRNA. If I will use --quantMode TranscriptomeSAM GeneCounts option, from which of the exons I will get the counts? Will star somehow sum them up?


Thank you very much

Alexander Dobin

unread,
Nov 26, 2017, 2:15:09 PM11/26/17
to rna-star
Hi Alex,

the "exons" with the same transcript_ id belong will be arranged into the transcript. STAR will use this information to extract the splice junctions and output transcriptomic alignments with --quantMode TranscriptomeSAM .
When counting reads per gene with --quantMode GeneCounts, STAR will sum the alignments overlapping the exons with the same gene_id.

Cheers
Alex

Grant

unread,
Nov 27, 2017, 11:37:47 AM11/27/17
to rna-star
Thank you Alex, you are very helpful!

It would be nice if you could implement gff-gtf conversion tool in STAR, I'd personally feel safer with a tool developed within STAR.

Thanks

Alexander Dobin

unread,
Nov 27, 2017, 10:08:12 PM11/27/17
to rna-star
Hi Grant,

that's a good suggestion - will put it on my TODO list, which is unfortunately growing very long.

Cheers
Alex
Reply all
Reply to author
Forward
0 new messages