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Hi,
I was trying to test the software to extract nuclear coding genes with introns, but apparently, it retrieves only the first open reading frame and misses the rest of the coding gene.
Is there …
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## The need
In the case of introns (eukaryotes and some of their viruses), the estimated genomic redundancy can be highly inflated, wrongly indicating that the quality is bad.
## The solution
…
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Hi,
I found some extremly long introns in spaln results (when mapping protein sequences to genome), some are ~1Mb, is there a way to limit intron length when running splan?
![image](https://user…
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Hi there,
I was testing LiftOff and LiftOn to see which one is "best" for genome annotation. I was looking at some RefSeq genomes, lifting the brown-headed cowbird and red-winged blackbird onto the…
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I could unzip
cds+introns.fa.gz
but not
cds+introns+utrs.fa.gz
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Just trying to understand the QTL experiment a bit more.
The [QTL dataset](https://www.giladlab.uchicago.edu/data/jointLCL/) is unavailable.
From the paper it seems unclear whether p=600 or p=7…
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**I have read the paper (https://doi.org/10.1038/s41467-020-15171-6)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about**
- align
- correct
- collapse
…
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hi there,
I'm experiencing a bug that's the same as an [issue that was closed back in November](https://github.com/Bioconductor/VariantAnnotation/issues/76), but it still seems to be a problem.
…
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Hi everyone,
I am trying to analyze some transcriptome assembly I created via Trinity. Considering the final nucleotide sequence is called .cds, does transcdecoder exclude introns? Because I am loo…
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Hi Danny,
Thanks for putting together such a cool program. I am working on mapping structures in introns using SHAPE experimental data, do you have any recommendations for search parameters, or do…