How the counts of a small RNA are calculated

[arazit]

Hi Mike,
We noticed that miRNA clusters that contain identical mature miRNA sequence have different counts for that mature miRNA.
Can you explain how the counts are calculated?
Sincerely,
Tzahi Arazi

[MikeAxtell]

Hi Tzahi, The counts at a given locus , and for the 'major RNA', are the number of aligned reads at that specific locus. For multimapped sequences, like many mature miRNAs, the counts are just those that were aligned at that specific genomic location. They will not usually be equally distributed across all possible alignment positions because of the way the script decides on best placements for multimappers (see Johnson et al for details).

On Tue, Oct 2, 2018 at 3:47 AM arazit ***@***.***> wrote: Hi Mike, We noticed that miRNA clusters that contain identical mature miRNA sequence have different counts for that mature miRNA. Can you explain how the counts are calculated? Sincerely, Tzahi Arazi — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#83>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGiXiYjhHa_Z4xx5h5TDLp63asO2CMOzks5ugxoggaJpZM4XDfw9> .

-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell