Closed tarakaramji closed 1 year ago
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
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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?
Would like to add a simple cross-check against miRBase mature miRNAs in the next major release. Make it so.
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.
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