Hi Everyone,

I have smallRNA seq data from 7subjects and I am trying to align them using mirdeep2 aligner. The bowtie log file shows the following stats:

# reads processed: 194093

# reads with at least one reported alignment: 70610 (36.38%)

# reads that failed to align: 112171 (57.79%)

# reads with alignments suppressed due to -m: 11312 (5.83%)

My question here is that 57.79% of reads failed to align which is very high. I have done adapter trimming and the fastqc looked fine after adapter removal. Did anyone use mirdeep2 to align smallRNA seq and had the same problem?