For microRNAs you don't need cufflinks. The precursor is normally less than 100nt in length and normal RNA-Seq reads should be longer. Assure that you clip the adapter of your reads correctly (since they are longer than the molecule of interest) and use a regular mapping algorithm (e.g. Bowtie, segemehl, BWA, STAR, etc.). Assure that you turn on the multiple mapping paramter, since small RNAs are known to have multiple copies in the genome. Without multiple mapping, all these multi-copy genes would be filtered out.
I am currently working on miRNA NGS. I tried to use Cufflinks but it seems that it is set so that you will only get the "exon" reads. I am currently using annotation from UCSC and bedtools intersect to annotate my reads. Then using a simple bash script to count the reads/miR (or tRNA, piRNA....etc).
For microRNAs you don't need cufflinks. The precursor is normally less than 100nt in length and normal RNA-Seq reads should be longer. Assure that you clip the adapter of your reads correctly (since they are longer than the molecule of interest) and use a regular mapping algorithm (e.g. Bowtie, segemehl, BWA, STAR, etc.). Assure that you turn on the multiple mapping paramter, since small RNAs are known to have multiple copies in the genome. Without multiple mapping, all these multi-copy genes would be filtered out.