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