Question: Get miRNA expression from RNA-seq
1
gravatar for bharata1803
3.2 years ago by
bharata1803420
Japan
bharata1803420 wrote:

Hello,

I have Fasta file from RNA-seq experiment. My supervisor gave me a list of micro RNA sequence. Is it possible to do alignment and then calculate the micro RNA expression? I have read the other post that the experiment protocol for RNA expression is different from the micro RNA expression. The fasta source write that the experiment is for Total RNA. Does it mean it will include the micro RNA? Any suggestions? Thank you all.

rna-seq alignment • 1.1k views
ADD COMMENTlink modified 3.2 years ago by BioRyder160 • written 3.2 years ago by bharata1803420
2
gravatar for Sean Davis
3.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Generally, the protocol for miRNA is quite different as it must include a "spacer" to get sequences long enough to sequence.  In other words, while you may be able to get other flavors of non-coding RNA (lncRNA, unprocessed miRNA), processed miRNA are not going to be present in your library.

ADD COMMENTlink written 3.2 years ago by Sean Davis25k
1
gravatar for BioRyder
3.2 years ago by
BioRyder160
India
BioRyder160 wrote:

Normally miRNA read length will be 50bp including adapter.the possibility of miRNA read presence in RNA seq is all most null. Because the difference in protocols.But you can get other RNA like tRNA,rRNA from mRNA seq.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by BioRyder160
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