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?
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?
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.
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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?
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?
I have no detail knowledge of that tool.