Dear All, I've been using the pipeline for a while for mouse and human miRNAseq data. While the mouse genomes didn't have any issues, the human genomes are having a peculiar one. Specifically, the reference miRNA mapping rate have been poor (see attached multiqc plots). Incidentally, the difference in the plots arose from a University bioinformatics core who generated the data, used the

-profile 'qiaseq'

parameter for version 2.3.1 but when I used it, it didn't make any difference in the mapping rate. I've been trying to solve this issue for 3 days, without any solution. Any help is much appreciated. Thanks in advance. P.S - Since the 2 runs differed in number of samples but sample11 is common between them.