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There has been the request to display the coverage of an exon upon request, or more specific if the coverage of the exons of a gene have at least X coverage, or if an exon has insufficient coverage.
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**Describe the bug**
I am test running Chanjo2 in preparation for further demonstrating and discussing (finally, hopefully) putting it into production.
Reports looks fine, and MANE info looks go…
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Hello, I would like to see which specific exons undergo alternative splicing for these genes. Taking SE.MATS.JCEC as an example, I’m currently using the Ensembl website to examine all transcripts of t…
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### Describe the bug
The `get_adjacent_exon` method needs to be updated to consider edge cases where `start` or `end` occurs along the boundaries of the exon.
### Steps to reproduce
N/A
### Expect…
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Hello,
I am using your visualization tool for RNA-seq data analysis and have a question about how exon inclusion is depicted. The image shows two graphs in different colors (purple on top and red o…
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As the title notes, a GTF returned by `export_gtf` is incomplete and should contain entries for transcripts.
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**Are you using the latest release?**
funannotate v1.8.17
**Describe the bug**
When I run funannotate predict I get an error
[Oct 15 05:17 PM]: Training Augustus using BUSCO gene models
Error: …
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Thank you for your tool. I encountered some issues while running rMATS. When examining the SE.MATS.JC.txt file to analyze skipping exon events, I filtered the data using 'FDR < 0.05, IncLevelDifferenc…
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Congrats for your paper! DeltaSplice looks very promising.
I was testing `pred_deltassu.py` using my own toy data and noticed that this script works well for any single nucleotide variant (SNV), b…