Using Bowtie for hsa-miRNA Reads: Should I Restrict Reverse-Complement Mapping?

Question

[MH85]

Hello, everyone

I have miRNA reads that I map onto miRbase hsa reference using bowtie. My objective is expression profiling. I'm considering whether to use the --norc option to restrict reads from aligning against the reverse-complement reference strand. My current bowtie parameters are:

bowtie -k 1 --seedmms 1 --best --seedlen 25

Could anyone share insights or recommendations on whether to use the --norc option in this context? I am asking because some hsa-miRNAs are reverse-complement to each other. For example, hsa-miR-103a-3p is reverse-complement to hsa-miR-103b.

>hsa-miR-103b
TCATAGCCCTGTACAATGCTGCT
>hsa-miR-103a-3p
AGCAGCATTGTACAGGGCTATGA

Thanks a lot in advance