Microrna Alignment And Output

Question

[Hamilton]

Post alignment of microRNA and mapping against Mirbase I have a column ID with the precursor as well as the mature microRNA name, on parsing the column I have the list with the mature microRNA which has duplicates with different read counts. Which one of the microRNA should I consider for the the downstream analysis as some of the names are in duplicate. Please suggest.

[Jeremy Leipzig]

duplicate because they are the same mature sequence from different species?

[Hamilton]

nope they are all same species. mmu all mouse.

Answer 1

[Rm]

Refer to this post.

My two cents: Same mature miRNA with different precursors as they map to different chromosomal locations. I guess treat them as separate with same counts, unless you are interested in a miRNA of a specific location.