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Hello,
I am working with a species that has huge introns (>30kb). I have aligned reads to the genome using a very high cut off (and I will probably have to go even beyond that). I attempted to asse…
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Hi, is it possible to stringently require all introns considered by braker to have support in the RNA-seq data provided? I am finding that braker is adding a lot of introns to gene predictions that ar…
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Dear @lh3 ,
Thanks for developing miniprot. I have been trying it out & it is extremely useful.
I had an idea for a possible enhancement... it would be very interesting to be able to provide kno…
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Hi,magicblast take small introns (peaks at 23 bp) in my genome as deletions, and I cannot find any way to solve it, do you have any great suggestions?
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Hello,
I generated my own annotation via GTFtools from GENCODE's v35 GTF file. I used it to run iREAD on 33 samples, which were all aligned to GENCODE's v35 reference genome using STAR. For each sa…
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Hi, @lh3
It seems a lots of long-intron protein mapping in the `miniprot` result, can we use some parameters to filter out these? Its size smaller than the default `-G` 200k. Did it confused by th…
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![图片](https://github.com/yefei521/Tetrahymena_Genome_annotation_V2024/assets/61307610/6e81f39e-96f5-4e8c-8ded-a0f0ecc8cda3)
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Hi,
Thank you for your interesting tool! :)
I'm interested in calculating dn/ds for rickettsia sequencing data and i can't find a table of transcripts of this spp. from Ensembl BioMart. I'm wonder…
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Hi
The **.stats** file, mentions a number of novel exons and a number of novel introns identified. Is there an easy way to get the coordinates of these regions?
```
e.g.
Novel exons: 16055/6…
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Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads …