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Hi,
I am running breseq to identify mutations in E. coli samples and I've noticed that a few times mutations appear where in the gene_name column I have something with the format gene1|gene2. I could…
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Dear,
I have selected the zebrafish database. All genes in my data are in lowercase, which is consistent with the database, but some of my data are sccafold numbers. Will this affect the analysis? …
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Hi developers,
This is a great tool to study convergent evolution. I have several questions:
1. RERcoverge requires that all gene trees have the same topology (same with the species tree if I un…
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Hi Richard - hope this is my last question for you. I uploaded my output files to the server. Is there a way to extract the information in the 'gene cluster table' and 'sequence alignment window' to o…
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You can smelt a gene sample from Gendustry in the furnace and have it turn into a blank gene sample in the EU2 furnace. It outputs a blank sample in the output slot and turns the sample in the input s…
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## Overview
We have been discussing this recently. There seems to be some duplication of efforts between the OMIM ingests [used by `mondo-ingest`](https://github.com/monarch-initiative/omim) and [use…
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Hi, I am analyzing a dataset with several samples that I plan to use for downstream analysis of both gene level and transcript level analyses. I noticed an issue with the gene count matrix generated…
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## Overview
I found one instance where there is an association with multiple mapping keys in `morbidmap.txt`.
```tsv
Phenotype Gene Symbols MIM Number Cyto Location
Neurodevelopmental disorder w…
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Hello !
I have a question more than an issue, but maybe you can help me,
I am annotating a dozen of arthropods assemblies from a same genus with braker3 (arthropoda prot + RNAseq data),
For a…
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Dear Dr. Qiao,
Of the output files from DupGen_finder, I found that the number of genes in the file 'xxx.wgd.pairs' (after deduplication) is equal to the number in the file 'xxx.wgd.genes'.
But …