it is my first time to analyse miRNA data. I have some miRNA data , species: bos_turus, single end, read length is 75bp, I double checked with sequencing guy, they said I should trim adapter of the Illumina HiSeq 2000 miRNA protocol, 3' trimmed. I have tried to trim adapter using this command:
trim_galore -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --stringency 6 001.fastq
Then I mapped my 001_trimmed.fastq using hisat2 . I got only 44.23% overall alignment rate. I have checked my read length distribution after trimming, the read peak is at 44bp.
I have no idea why I got so low mapping read. Could anyone please help me with this?