I have been doing microanalysis of zebrafish data using the following pipeline steps. 1) Cutadapt default scripts for 3 'adapter removal. 2) Checking quality with FASTQC of the unpaired micro RNA reads in question. 3) I used zebrafish version 10 genome as the reference sequence- used bowtie default scripts for both genome indexing and subsequent alignment. 4) Zebrafish whole-genome GTF has been used for subsequent counting with HTSeq using default parameters to align by coordinate and position. After read counting 5) I used DESeq2 for differential gene expression analysis. Based on these steps I have been able to map over 200 microRNAs out of over 354 mature miRNA sequences present in the latest version of mirbase22. MY question is can anybody help me out to use specific parameters in each of the steps to ensure maximal capturing of miRNAs?
