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I believe this to be a sequencing artifact rather than an issue with DADA2, but perhaps you have advice on how best to mitigate this issue computationally. I did an experiment where I basically challe…
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There are a bunch of different ways to refer to a human gene, but we want to use HGNC gene symbols in our interfaces in Corpora. This gives us human-intelligible labels. Everyone knows what TP53 is, b…
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I've been an ardent user of kb_python since it's release but I've just noticed some striking differences with the lamanno flag generated reference versus the "normal" reference generated from the same…
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Hi partis team
This might be a weird question, but is it possible to use partis to annotate chicken antibody sequences? The maturation process is quite different and is based on diversifying gene …
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Hi @lucventurini,
during mikado prepare I'm getting a lot of warnings:
```
2020-10-22 11:58:37,788 - Checker-3 - transcriptchecker.py:342 - WARNING - check_orf - Checker-3 - Invalid ORF(s) for …
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Dear developers:
Thanks for developing this software. Recently I was trying to identify NLR genes in tomato reference genome Heinz 1706 SL4.0 and found that NLR-parser returned 242 NLR candidates u…
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Hi Mick
I've tried to run this pipeline and am able to get to the splign step which produces directories entitled splign/CDS with a subdir for each transcript. However I cannot see where these dire…
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Original comment by: ValWood
Some pseudogenes have changed status and need "warning, previously annotated as pseudo"
and GO annotation.
If a gene has a single frameshift, it probably isn't go…
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Hi Davi,
I'm using OrthoFinder for the first time to compare some ant genomes and it is a very nice tool!
I just have a question (maybe silly) about how not using a single variant per gene could a…
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While the PHMM is filtering out most non-homologous loci, some match well enough to make it through, but they have a frameshift mutation. Need to add a further function to check for this.
Potential…