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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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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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## 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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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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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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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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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…
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Hi~ Andrey,
I am using IsoQuant's v3.3.1 Reference-base model for Isoform annotation in polyploid species and updating my gff3 annotation file. To check the accuracy of the annotation, I visualized t…
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Hi there!
I would like to validate experimentally some fused genes. For doing that, I should keep the most expressed isoform for each gene. I would like to know how FusionInspector decides the iso…
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Hi author,
Thanks for developing this brilliant isoform analytical tool!
May I ask where could I find the splice junctions of annotated isoforms and the types of alternative splicing events fro…