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lncRNA Prediction tool

Hello, I have a RNAseq data, I want to predict lncRNA from this data. Please help me in this regard which tool should I use.

Thanks!!

Best

rna-seq next-gen
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updated by Tm Tm • written by georgians • georgians

Are you sure, that your data contains lncRNAs? Which kit you have used for library preparation? Because if it enriches polyA then in that case you cannot expect lncRNA in your sample.

Can you also reveal on which organism you are working?

• 1 views • link
written by Tm Tm

Not sure if there exists any specific tool for this.

in a nutshell: what people usually do is to align all reads to a genome, filter out those that match protein-coding and the long ones that do not are the lncRNAs . Alternatively you can assemble all your reads, predict ORFs on them and those that are 'long' and does not seem to have a valid ORF are likely the lncRNAs

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written by lieven.sterck lieven.sterck

1 answer

you are working on human genome then can try using lncFunTK or UClncR. Alternatively you can explore previous biostar post and this article where they have identified lncRNA from wheat transcriprome.

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written by Tm Tm

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