I have used HISAT2 for mapping my RNA-seq data (150bp, paired-end, Illumina platform). I would like to compare my results with results from RNA-seq data obtained from SOLiD sequencing. I found out, that for SOLiD, generally, BWA or BOWTIE was used.
Is there any reason why HISAT2 should not be used for SOLiD data? I plan to pre-treat the data (convert the colour space and trimm it based on quality check).