question about using unmapped reads from Hisat2

[dingxm]

I have bam files from the Hisat2 aligner which only included the mapped reads. I extracted the unmapped reads from the original fastq based on the bam files and used the unmapped reads as the input files of imrep. My concern is the mapped reads from hisat2 may have some useful information. Is that ok only use the unmaped reads? is there anyway i can used both the mapped only bam and unmapped fastq as the input files? Thanks