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This variant https://www.genomenexus.org/variant/17:g.59926628T%3EC gets annotated as Intron but is actually Splice.
I'm guessing it is because `splice_polypyrimidine_tract_variant` is missing in a…
inodb updated
2 years ago
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Hi there,
Thanks for the wonderful new tools! I have a question about the output of the script [new_annotator_with_skipping.py](https://github.com/landau-lab/ONT-sc-splice/blob/main/junction_annota…
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Hi, I want to know if you implement this algorithm from the paper [SplicePort—An interactive splice-site analysis tool] ?
ghost updated
5 years ago
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Possibly fix this issue
```bash
Command error:
Traceback (most recent call last):
File "/opt/conda/envs/splicing-pipelines-nf/bin/bamCoverage", line 5, in
from deeptools.bamCoverage impo…
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The HGVSp field is empty for variants in the intron or in the UTR. The correct HGVS description for not expecting a change on protein level would actually be `p.(=)`. In case the variant is inside a s…
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### Description
Seems that Outrigger needs .chromInfo file but can't find it
There is also a conflit from Ensembl vs UCSC chr naming convention
### Steps to Reproduce
1. Alignwith STAR (OK) us…
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- [ ] Finish molQTL plotting scripts and plot coverage data for bunch of Colocalized QTL effects
- [ ] Add more GWAS. Need to edit some scripts to accommodate binary outcomes for some gwas... see (…
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Hi rMATS team,
I wanted to discuss a discrepancy I've encountered between the results obtained from rMATS-turbo analysis and what I observed in the Integrated Genome Viewer (IGV) while examining RNA-…
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splicePrior can equal 0.02 for more than one reason:
- The de novo splice likelihood is weak/null, or low.
- The de novo splice site creates an innocuous In Frame Deletion (IFD). It is also ambig…
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I'm using mpileup to compute the mutation frequencies of a list of known variant sites in RNA-seq. For a small number of indels the AD numbers in the output are much lower than what I'm seeing in IGV.…