Question: miRNA analysis for de novo assembled RNA seq data
gravatar for adil.simply
2.3 years ago by
adil.simply0 wrote:

I am working on Plant RNA seq data and am interesting in predicting pre miRNA and miRNA. kindly suggest me tools where I don't need whole genome data, and the tool should work for plant RNA seq data. I used miRNAfind from softberry its standalone version is showing some error and online server accepts only limited number of sequences whereas my data consists of 2500 sequences which I need to analyze.


rna seq mirna prediction • 1.0k views
ADD COMMENTlink written 2.3 years ago by adil.simply0

You may try mapping validated miRNAs (mirbase for example) to your transcripts or to transcripts from mirgenes. But, in this case if RNA-seq library was not prepared as small-rnaseq library you can't find mature mirnas, short reads are not mirnas.

ADD REPLYlink written 2.3 years ago by Buffo1.8k
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