Question: How to aligne miRNA reads with transcriptomic reads
gravatar for Farbod
5.0 years ago by
Farbod3.3k wrote:

Dear Friends, Hi. I want to ask you about mapping the miRNA reads to transcriptomic reads of the same species in the absence of genomic data.

I have 3 males and 3 females miRNA-seq read sets generated from Illumina Hiseq2000 platforms of a non model fish (no genome, so de novo).As my fish is non-model, I have run RNA-seq for that (from same tissue and with 3 biological replication for each sexes) , too. And assembled my RNA-seq using Trinity software. Now I have my reference assembly Trinity.fasta file created using all my RNA-seq reads (paired-end 101 bp reads)

How can I map (or aligne) my miRNA to my RNA-seq for target prediction ? I was thinking that mapping the miRNA to transcriptome of a species would be more effective than mapping them to Genomic data for target prediction but now it seems it is not so painless !

Thank you in advance

rna-seq • 1.3k views
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