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I think it would be possible to adapt to [`TreeSummarisedExperiment`](https://github.com/fionarhuang/TreeSummarizedExperiment).
Things checked:
- It is possible to subset the `TSE` object.
- It…
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Hi,
I would like to use the spike-In (using the eption -spk).
Can you explain me more how to use it
What we need in input to use it?
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Hi @naumenko-sa,
for the [problem](https://github.com/chapmanb/bcbio-nextgen/issues/1395) with the report we can discuss here.
That report is a template that won't work in all analysis sadly. Can …
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- [x] GO:0035195 gene silencing by miRNA >>>> change label to 'miRNA-mediated gene silencing' to match other terms in the same branch
- [x] fixed definition miRNA-mediated gene silencing: to "An RNA…
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Dear Daniel Liu.
I am revisiting my code for miRNA analysis prior to publication.
I am double checking that the deduplication occurs as it should.
I grep'ed two UMI tags and wrote out the …
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Hello,
This is Ketaki Bhide from Purdue Bioinformatics Core. We are working with Zymo for one of our collaborator's MultiOmics project.
We are trying to repeat analysis for couple of samples as …
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Can mirge3 output an annotation file (chromosome, start position, end position) for all miRNAs detected? Can mirge3 output the canonical mature miRNA?
I've created a script that examines the human …
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Hello! I've been using miRge for a while and have recently detected some discrepancies between what I expected and what I obtained, and I've been trying to understand the reasons but haven't been able…
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2 files (and checksums) available at
https://gannet.fish.washington.edu/seashell/wd/ln/
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Hello again @arunhpatil ,
I'm currently working on modifying miRge3.0s alignment behaviour for my own purposes and I've noticed a routine in the code which may have the potential to output non-opti…