Separating the known miRNAs from the new clusters identified in ShortStack

[tarakaramji]

Hi,

As per the instructions, i have run the pipeline using the denovo-clustering and after which I provided the loci file of known miRNAs from miRBase. How am I supposed to get the ones which are not known (novel miRNAs)? Please suggest Thank you

Regards, Ramji

[MikeAxtell]

Hello, thank you for your message.

ShortStack is not designed to explicitly check against previous annotations. You could use a tool like bedtools intersect to find overlaps between de novo loci found by ShortStack and pre-existing annotations.

Best Wishes, Mike

On Sun, Oct 28, 2018 at 7:20 AM Taraka Ramji Moturu < notifications@github.com> wrote:

Hi,

As per the instructions, i have run the pipeline using the denovo-clustering and after which I provided the loci file of known miRNAs from miRBase. How am I supposed to get the ones which are not known (novel miRNAs)? Please suggest Thank you

Regards, Ramji

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMikeAxtell%2FShortStack%2Fissues%2F84&data=02%7C01%7Cmja18%40psu.edu%7Cc0c79afe88ca4bd7701c08d63cc75d33%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C636763224303625750&sdata=WUvNJL4WUipaTqQsPddzgpyZnNf13sC%2B0kDxLe14CQc%3D&reserved=0, or mute the thread https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAGiXiXZE46JgCsWncy_3rm6HmdcprvF8ks5upZL5gaJpZM4X96J-&data=02%7C01%7Cmja18%40psu.edu%7Cc0c79afe88ca4bd7701c08d63cc75d33%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C636763224303635746&sdata=CoF7%2Fo62%2F9EEANMnQzsImhX4zbanuO5apxwe7ya3Ba4%3D&reserved=0 .

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

[juancresc]

hi @MikeAxtell! Any hints about how to identify known mature miRNAs?

Right now I'm doing a blast search (-task blastn) using the MajorRNA column as query and mature sequences from miRBase as subject. Then, filtering out all hits with more than 2 mismatches and alignment length less than the mature miRNA length minus 2. From your own paper:

Defining a “conserved” miRNA is an inherently slippery concept. When applied to miRNAs, conservation generally refers to the accumulation of identical or near-identical (one or two nucleotide differences) mature miRNA sequences, although the miRNA* and some flanking hairpin sequence also sometimes demonstrate conservation

Do you think this approach is ok?

[MikeAxtell]

Would like to add a simple cross-check against miRBase mature miRNAs in the next major release. Make it so.

[MikeAxtell]

ShortStack4 implements a knownRNAs file that nucleates MIRNA searching at genomic locations where user-provided RNAs are aligned to the reference genome. ShortStack4 is currently in alpha testing and can be accessed on the ShortStack4 branch.