<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>

CC BY-SA 4.0
2020-03-25T08:42:39.180Z
2020-03-25T08:42:39.180Z
Diango
<p>If literally all you have is the count info by gene, you can't magic up the isoform breakdown.</p>

CC BY-SA 4.0
2020-03-25T03:38:30.847Z
2020-03-25T03:38:30.847Z
swbarnes2
<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>

CC BY-SA 4.0
2020-03-24T16:32:04.353Z
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.
Ram RS
CC BY-SA 4.0
2020-03-24T18:36:38.337Z
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?
StupidWolf
<rna-seq><deseq2><rna><rna-alignment><rna-splicing>
Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
# 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?  

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## 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


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### 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.


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