miRNA analysis for de novo assembled RNA seq data
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.
Thanks,
ADIL LATEEF
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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.