small RNA Mapping Rate

[kumarage]

Hi,

Mapping small RNA for the first time and my input data are Illumina 50bp single end reads trimmed using fastp.

Following one of the Google forums on "small RNA", used the setting in STAR 2.7.11b as: "--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1" --winAnchorMultimapNmax 1000.

In final.out,

Number of input reads | 24962381
Average input read length | 28

UNIQUE READS:
Uniquely mapped reads number | 6932831
Uniquely mapped reads % | 27.77%
Average mapped length | 24.40
Number of splices: Total | 3987
Number of splices: Annotated (sjdb) | 3987
Number of splices: GT/AG | 3881
Number of splices: GC/AG | 28
Number of splices: AT/AC | 9
Number of splices: Non-canonical | 69
Mismatch rate per base, % | 0.03%
Deletion rate per base | 0.00%
Deletion average length | 1.00
Insertion rate per base | 0.00%
Insertion average length | 1.04

MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 16045341
% of reads mapped to multiple loci | 64.28%
Number of reads mapped to too many loci | 1837002
% of reads mapped to too many loci | 7.36%

UNMAPPED READS:
Number of reads unmapped: too many mismatches | 1
% of reads unmapped: too many mismatches | 0.00%
Number of reads unmapped: too short | 16847
% of reads unmapped: too short | 0.07%
Number of reads unmapped: other | 130359
% of reads unmapped: other | 0.52%

CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%

I assume "Uniquely mapped reads %" is low because turning the --alignIntronMax 1 controlling the mapping across splice junctions. Unmapped percentage is low at "0.52%". I have to use this data to study micro RNA behavior in Disease vs Control. Is these stats look like an acceptable mapping. If not are there ways I can improve the results?