Hi everyone. I'm having troubles analyzing some miRNA seq files.
First I used cutadapt to trim the universal adaptors. I confirmed that all adaptors and polyA were correctly trimmed by using fastqc. However, when i make the alignment versus my Homo Sapiens index the result is barely 12% (Which I think is very low).
I took the results of the alignment (around 300 IDs) and analyzed to obtain the differentially expressed miRNAs (around only 16)
I'm not an expert in the Field. I need help to increase the percentage of alignment and therefore the differentially expressed miRNAs.
Is there any suggestion to analyze it better?