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Hello,
Even with -overlap 0.0, Liftoff can generate overlapping exons (example : exon1 [400279 400378] exon2 [400378 400725])
How to avoid this ? Would it be possible to merge this kind of exons…
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https://github.com/tgen/jetstream_resources/blob/1a368800f42af8f57e9a8630f69b2018f81d6044/phoenix/create_gene_model.sh#L248-L249
This seems to produce the same exon for each transcript of the gene,…
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Hi!
I have 921 eukaryotic genome assemblies - from NCBI and literature - I would like to run ContScout on with nr as the database.
Running 5 assemblies initially, 2 completed successfully (run …
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Hello,
I'm analysing single-cell full-length RNA sequencing data. I would like to perform an analysis on alternative splicing exons, which has been mentioned multiple times in your research group's…
weib3 updated
4 months ago
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Hi @chunxubioinfor
I have checked the isoform_id from the gtf and isoform_id in salmon$counts, however, there is no difference between them. When I only use the isoform from iso-seq data instead of i…
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Not sure if this was intentional -- but currently can lead to some counterintuitive results:
```
In [9]: await cst.transcript_to_genomic_coordinates(
transcript="NM_002529.3",
exon_star…
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**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
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Hello Alejandro
Thank you for developing this tool to convert the TOGA bed output to GTF. I need a GTF file to perform several downstream analyses, so this tool is exactly what I need! I appreciate…
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@ShreyasDasari the length of the introns is incorrect. Please note that both the start and the end coordinates are on the exon. So the intron length is one less that what you computed. Please fix it. …