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Dear authors,
As I am working with squamate genomes I wanted to test retraining the TOGA models for this group, and I have some questions regarding this. Any help is much appreciated!
1) I was f…
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Hello! First of all thanks for this great work!
I'm reading the `CellphoneDB`'s documentation, and I find in the `protein_input` section c, it's said that the membrane and secreted proteins are not…
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Hi,
I'm using breseq to call mutations in populations resulting from a lab evolution experiment. I encounter some mutations in intergenic regions, listed by breseq as geneX/geneY . In the column gene…
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Hi Danny,
I have a question regarding how `rf-count` operates with alignments/SAM flags. Based on output from `rf-rctools view` I am seeing fewer (T->C) mutations {rfcount_7sK.jpg} (no positions > …
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**Question**
First of all, thank you for this wonderful tutorial! It has been immensely helpful in dealing with single-cell datasets, and I've gained valuable insights from it.
I've been struggl…
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Hello processor, I came across some problems when I processed the results of the Pseudogene Pipeline. Many of the pseudogenes identified by this pipeline overlap with gene regions. I processed the inp…
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Combined 01_ and 02_createObjectwithmetadata
-Remove pseudogenes & model genes
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There is no "proc_pseudogenes.bed" in the TOGA output files.
At first, I found a “#” in front of the 752 line of code in toga.py, I thought I found the reason. However, after deleting "#" and re-subm…
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Hi thank you for your nice tool.
I've encountered problem while using ggcaller v1.3.4. (error log is below the description part )
I created conda environment and installed ggcaller following offic…
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I ran the following command:
`hyphy busted --alignment $msa_file --tree ${tree_dir}/${OG}.pruned_tree.labeled.txt --branches test --output $outfile > $stdoutfile`
and received an error with the …