So I'm basically getting these 'successfully assigned reads" of around 30 - 45%. When I did STAR I got alignment reads of like 70-80% which is really good. I know that FeatureCounts counts the amount of reads (achieved in STAR) appeared to overlap with known genes. And so it's normal that it's lower than the percentage I got for the STAR alignment. However, I don't really get how it gets this low. Is there maybe a fault that I could've prevented while doing fastqc? Like some trimming or something? Would it then increase in percentage? (Assigned reads). And secondly, if I don't need to do anything. What can I give as an explanation for this low percentage? Can I just proceed with my analysis?

Load annotation file /mnt/storage/data/resources/genomes/hg38/hg38.ref ... ||
||    Features : 831683                                                       ||
||    Meta-features : 28278                                                   ||
||    Chromosomes/contigs : 367                                               ||
||                                                                            ||
|| Process BAM file C1.bam...                                                 ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 35409751                                                  ||
||    Successfully assigned reads : **13794555 (39.0%)**                          ||
||    Running time : 0.47 minutes                                             ||
||                                                                            ||
|| Process BAM file C2.bam...                                                 ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 33118524                                                  ||
||    Successfully assigned reads : **14166283 (42.8%)**                          ||
||    Running time : 0.45 minutes                                             ||
||                                                                            ||
|| Process BAM file S1.bam...                                                 ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 31476163                                                  ||
||    Successfully assigned reads : **13113126 (41.7%)**                          ||
||    Running time : 0.42 minutes                                             ||
||                                                                            ||
|| Process BAM file S2.bam...                                                 ||
||    Single-end reads are included.                                          ||
||    Assign reads to features...                                             ||
||    Total reads : 38025040                                                  ||
||    Successfully assigned reads : **12831852 (33.7%)**                          ||
||    Running time : 0.51 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
|| Summary of counting results can be found in file "all.counts.summary"