Question: Identify the isoform of a transcript using RNA Seq data
0
gravatar for aggregatibacter
2.7 years ago by
Bonn, Germany
aggregatibacter110 wrote:

Hi,

my favorite transcript is supposed to consist of 12 exons (it was only described in germ cells, not in somatic tissues). Thus, I want to check what isoforms are actually expressed in my (somatic) tissue of interest.

I have paired-end RNA Seq data from a larger number of samples. I would like to use this dataset to shed light onto the isoform.

Thus far, I have aligned my reads using STAR, and counted exons using featureCounts. Seemingly, only a few exons are expressed, but quite consistent over all samples. There is no described isoform of the transcript that looks like what I have.

How would you suggest to go from here to obtain a consensus sequence? Do I need to assemble the whole transcriptome, or are there any shortcuts I can take, as I am only interested in a single transcript?

Many thanks!

rna-seq • 1.3k views
ADD COMMENTlink modified 2.7 years ago by EagleEye6.3k • written 2.7 years ago by aggregatibacter110
2
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

I'd subset the alignments to contain only that regions and then run stringTie.

ADD COMMENTlink written 2.7 years ago by Devon Ryan90k

That sounds like a great idea, many thanks, Devon!

ADD REPLYlink written 2.7 years ago by aggregatibacter110
0
gravatar for Manvendra Singh
2.7 years ago by
Manvendra Singh2.0k
Berlin, Germany
Manvendra Singh2.0k wrote:

Did you try running Cufflinks2 RABT assembly; I would suggest you to run in both mode; default and RABT and see if you can catch your desired isoform

ADD COMMENTlink written 2.7 years ago by Manvendra Singh2.0k
0
gravatar for EagleEye
2.7 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

These posts might give you some idea,

A: How to determine alternative splicing read counts

A: workflow/tool for alternative splicing

ADD COMMENTlink written 2.7 years ago by EagleEye6.3k
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