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Hello,
I am trying to use FLAIR to look at transcript isoforms of FCGR2C with Nanopore cDNA sequencing. FLAIR appears to be failing to pick up isoforms showing retention of the final intron (which…
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## Details
**Created by:** myGlygen
**Feedback from:** myGlyGen@gmail.com
**Assigned to:** myGlygen
**Priority:** normal
[Open Note](https://app.pageproofer.com/to/note/351188)
## Note
> I think…
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Need to curate some alternative transcript examples for Chado loading
can do some from the gene expression list:
gene expression, alternative splicing (3)
gene expression, alternative transcri…
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Hello @EricKutschera,
is there a way to do this `classify_isoform_differences.py` for all isoforms? not doing individually for each isoform so that I have at the end all isoform in a single tsv fi…
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Funannotate final gff3 has only one transcript information per gene. It doesn't provide alternative splicing/isoforms in the gff file?
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## Motivation
Currently gene lengths are calculated using GTFtools algorithm of "merged" length of isoforms. It was brought to our attention by @jychien that these may be unstable across Genecode v…
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We're interested in quantifying isoform specific stability with a custom set of 3'UTRs
If we were to tweak the bam2bakR pipeline, supplementing a custom set of isoforms as separate ‘genes’ to a sta…
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There has been a substantial interest in a Whippet feature to use all edges to produce full isoforms.
- [x] Alter annotation support to load all known edges.
- [ ] Build/filter isoforms for legitimate…
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For tools such as `bambu` and `isoquant`, they produce an extended gtf including the novel isoforms which are not accompanied by a fasta file containing the sequence information. Is the fasta file req…
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How do isoforms relate to genotypes?
This genotype looks like it's isoform specific because the three isoforms of prp10 have different sequences:
https://www.pombase.org/genotype/prp10-1-A1089V,S1…