Get miRNA expression from RNA-seq

Question

[bharata1803]

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.

Answer 1

[Sean Davis]

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.

Answer 2

[BioRyder]

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.