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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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Hi, I'm looking to predict genes for my insect genome. For most genes the prediction is working out good, but egapx is missing predictions for some species specific, single exon genes (experiementally…
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Hi, I'm running Isoquant 3.4.1, I found that the novel genes predicted by Isoquant in Experiment1.extended_annotation.gtf doesn't have CDS information.
Here is my several lines of Experiment1.exte…
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### Ask away!
Hi, I would look at transcript usage but all transcripts are "unknown".
The file `transcript_processed_feature_bc_matrix/features.tsv.gz` contains only "unknown" transcripts.
```…
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This smells like maybe a multiprocessing bug, I'm not sure what else would cause this to happen. I'm seeing cases where a unique read (only appears once in input, no secondary/supplemental alignments …
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I might have mentioned it before, but there is only a single node with the category `biolink:Exon`: a node with the name `Exon`. I think either the ETL-ing of whatever KP has exon info is borked, or s…
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Hi,
I'm having issue with checkGTF when running on gtf file dowloaded on Genbank database :
Here the GTF file :
```
#gtf-version 2.2
#!genome-build ASM3821986v1
#!genome-build-accession NCBI…
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Hi,
I am using SUPPA to analyse DAS in rice.
My gtf file was generated from ESPRESSO:
# ESPRESSO version: 1.4.0, source code commit: unknown
Chr07 annotated_isoform transcript …
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### Describe the bug
A Transcript Segment object is currently not being created when a genomic coordinate that occurs between exons is supplied to start or end.
### Steps to reproduce
1. Select Tr…
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Hi,
We used Helixer to predict genes in plant genome assemblies we have constructed. Approximately 30k genes were often predicted and complete BUSCO scores are always >95%. It seems prediction accu…