Should i use Stringtie gene count or transcript count as input for DESEQ2? What is difference between gene count and transcript count?

Question

[aaghodsinia]

Hi, so stringtie generated to coutns for me: a gene count and transcript count. Which one should I use as input for DESE2 differential gene expression analysis? What is the difference between the gene and transcript count?

Answer 1

[ATpoint]

Use gene level counts. This is what DESeq2 has been designed for. A gene level count is the aggregation of all transcript level counts. A transcript is an RNA written from a template DNA which we term gene. Genes often have multiple transcripts. Please read a book towards basics of genetics. I suggest you check the tximport package which can be of help reading the stringtie data into R and DESeq2.

[aaghodsinia]

Dear ATPOINT,

thanks for your reply. I am confused slightly with the results I am getting. I have one entry called: MSTRG.13580.

In the stringtie merged GTF file it has the 2 following separate entries 1. gene_id "MSTRG.13580"; transcript_id "MSTRG.13580.1"; -> with coordinates on chr19, 52415921 - 52426291 2. gene_id "MSTRG.13580"; transcript_id "ENST00000359924"; gene_name "BBC3"; ref_gene_id "ENSG00000105327"; -> with coordinates on 52415924 - 52426291.

I wonder why entry no 1 is not given the gene name BBC3, while entry no 2 is given BBC3? Arent they supposedly from the same gene since the 2 entries have the same MSTRG no of 13580?

[aaghodsinia]

Dear ATPOINT,

thanks for your reply. I am confused slightly with the results I am getting. I have one entry called: MSTRG.13580.

In the stringtie merged GTF file it has the 2 following separate entries:

Entry 1: gene_id "MSTRG.13580"; transcript_id "MSTRG.13580.1"; -> with coordinates on chr19, 52415921 - 52426291

Entry 2: gene_id "MSTRG.13580"; transcript_id "ENST00000359924"; gene_name "BBC3"; ref_gene_id "ENSG00000105327"; -> with coordinates on 52415924 - 52426291.

I wonder why entry no 1 is not given the gene name BBC3, while entry no 2 is given BBC3? Arent they supposedly from the same gene since the 2 entries have the same MSTRG number of 13580?

[ATpoint]

I have no detail knowledge of that tool.