question about merged miRNAs

mhalushka / miRge

miRge - microRNA alignment software for small RNA-seq data, now at v2.0

GNU General Public License v3.0

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question about merged miRNAs #35

Open hust-yyan opened 2 years ago

hust-yyan commented 2 years ago

Hi, I found merged miRNA in the annotation file, but they are in different locations of the genome, according to what criteria is merge done?If I want to count separately, can I assign expression values to each miRNA?Now I am doing eQTL research for miRNA, which requires the precise location of each miRNA in the genome, but merged miRNA makes me not know how to deal with it.

mhalushka commented 2 years ago

Hi. miRge3.0 does not distinguish between genomic locations when a miRNA has more than one site, such as let-7a. I know other programs do this, but I think their assignments are arbitrary. There is no information in a FASTQ that can help determine location when the sequence exactly matches more than one genomic sequence.

arunhpatil commented 2 years ago

Hi @hust-yyan, you can find the link to miRge3.0 here.