Question: Is Kallisto good for identifying non-coding RNA in a RNAseq data?
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gravatar for priyankaraina10
10 weeks ago by
priyankaraina1010 wrote:

Hi

I generated a co-expression map using Kallisto for aligning reads. However, after completing my analysis, when I checked the gene_biotype for the gene list, I only found 3% non-coding RNA. I repeated the analysis with another data from (Skymap), I got similar results.

My question is this normal or Kallisto is not good in aligning non-coding RNA.

Thank you

ADD COMMENTlink modified 10 weeks ago by kristoffer.vittingseerup1.4k • written 10 weeks ago by priyankaraina1010

Kallisto uses a transcriptome genome index, so you can only detect what is present in the annotation.

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

Adding to what WouterDeCoster said: (i) a lot of non-coding RNAs are relatively small, which means that depending on which sequencing protocol was they might not have been sequenced at all; (ii) they might also be repetitive leading to multimapping reads which I am not sure Kallisto would be able to handle even if they are kept by the mapper.

ADD REPLYlink written 10 weeks ago by A. Domingues1.8k

True Kallisto is better suited for long-noncoding RNAs (lncRNAs)

ADD REPLYlink written 10 weeks ago by kristoffer.vittingseerup1.4k

You typically map short RNA species sich as microRNAs against a microRNA-only reference such as miRbase to avoid axactly this probem.

ADD REPLYlink written 10 weeks ago by ATpoint13k

I don't think miRNA should be a problem with standard RNA-seq as the miRNA are typically shorter than fragments analyzed due the size-selection step in the library prepreation.

ADD REPLYlink written 10 weeks ago by kristoffer.vittingseerup1.4k

Sorry, I misread the initial question, thinking that OP was quantifying miRNA-seq instead of miRNAs from standard RNA-seq. You are right, standard RNA-seq typically does size-selection for non-short RNA species.

ADD REPLYlink written 10 weeks ago by ATpoint13k
0
gravatar for kristoffer.vittingseerup
10 weeks ago by
European Union
kristoffer.vittingseerup1.4k wrote:

Yes. Kallisto does not distinguish between coding and non-coding. It only requires that the transcripts are already annotated (so if you are looking for novel lncRNAs you should use a different pipeline).

What is the frequency of lncRNAs in the transcript annotation database to start with?

ADD COMMENTlink written 10 weeks ago by kristoffer.vittingseerup1.4k
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