Generating read counts for my microRNA reads for a non model invertebrate

Question

[karthic]

Hi, I have a set of microRNA raw data in the form of single-end reads. I did the quality trimming, adapter removal, length filtering etc. and predicted the known and novel miRNAs from the data.

Now inorder do to DE gene expression studies, I chose to do with DESeq. I have generated the count table using collapse_reads.pl script from mirdeep2 package. However I believe the counts are normalised, whereas DESeq expects raw read count.

Now I want to generate the read counts using htseq-count, but my organism does not have a genome and there is no gff table in mirbase for it.

So I am stuck and confused as to how to proceed further. Please suggest some approach.

Thanks KK