Answers.Body: <p>You can back to your bam file and use cuffdiff tools it is very able to do your job follow this to liks
  <a href="http://cole-trapnell-lab.github.io/cufflinks/manual/" rel="nofollow noreferrer">http://cole-trapnell-lab.github.io/cufflinks/manual/</a></p>
  
  <p><a href="https://github.com/Jeanielmj/bioinformatics-workshop/wiki/Differential-Analysis-with-Cuffdiff" rel="nofollow noreferrer">https://github.com/Jeanielmj/bioinformatics-workshop/wiki/Differential-Analysis-with-Cuffdiff</a></p>
  
  <p>My best</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-25T08:42:39.180Z
Answers.LastActivityDate: 2020-03-25T08:42:39.180Z
Answers.UserDisplayName: Diango
Answers.Body: <p>If literally all you have is the count info by gene, you can't magic up the isoform breakdown.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-25T03:38:30.847Z
Answers.LastActivityDate: 2020-03-25T03:38:30.847Z
Answers.UserDisplayName: swbarnes2
Body: <p>I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to achieve this?</p>
  
  <p>In literature, 9 different isoforms of my gene of interest have been reported. My colleague who does the wet lab experiments has identified 3 of those isoforms through western blotting in the fibroblasts that later got sequenced. There might be more isoforms in these fibroblasts.</p>
  
  <p>I will be grateful for any computational hint to identify gene isoforms from my dataset, irrespective if they are differentially expressed or not.</p>
  
  <p>Thank you in advance for your kind help.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-24T16:32:04.353Z
Comments.Text: What tool did you use for quantification? Most tools produce transcript level counts, so this should be a pretty straightforward task once you get a list of the identifiers of the transcripts you're interested in.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-24T18:36:38.337Z
Comments.Text: If you have only counts on a gene level, you might need to go back to the bam file to get the isoform quantification.. Something quick might be kallisto?
Comments.UserDisplayName: StupidWolf
Tags: <rna-seq><deseq2><rna><rna-alignment><rna-splicing>
Title: Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
ThreadText: # Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
  
  (Asked by: username_0 on 2020-03-24)
  
  I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to achieve this?
  
  In literature, 9 different isoforms of my gene of interest have been reported. My colleague who does the wet lab experiments has identified 3 of those isoforms through western blotting in the fibroblasts that later got sequenced. There might be more isoforms in these fibroblasts.
  
  I will be grateful for any computational hint to identify gene isoforms from my dataset, irrespective if they are differentially expressed or not.
  
  Thank you in advance for your kind help.
  
  **Tags:** rna-seq, deseq2, rna, rna-alignment, rna-splicing
  
  > **Comments:**
  > **username_1**: What tool did you use for quantification? Most tools produce transcript level counts, so this should be a pretty straightforward task once you get a list of the identifiers of the transcripts you're interested in.  
  > **username_2**: If you have only counts on a gene level, you might need to go back to the bam file to get the isoform quantification.. Something quick might be kallisto?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2020-03-25. Score: 2
  
  You can back to your bam file and use cuffdiff tools it is very able to do your job follow this to liks
  <http://cole-trapnell-lab.github.io/cufflinks/manual/>
  
  <https://github.com/Jeanielmj/bioinformatics-workshop/wiki/Differential-Analysis-with-Cuffdiff>
  
  My best
  
  
  ---
  
  ### Answer by username_4 on 2020-03-25. Score: 1
  
  If literally all you have is the count info by gene, you can't magic up the isoform breakdown.
  
  
  ---
  
  