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Hi Ben,
Apologies for the multiple questions. I ran singlem separately on my metagenome reads and my MAGs. I then separated each marker and clustered them using the default species-level identity. …
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Hi,
Running LACHESIS in the below way did not provide the expected chromosome numbers because I got 115 groups.
```
/usr/local/bin/Lachesis lachesis.ini
/LACHESIS/src/bin/CreateScaffoldedFasta.…
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- [ ] concatenate and dereplicate phaeo proteins (or contigs?)
- [x] Use Salmon to map Tara meta T
- [ ] look at SNPs for pop gen?
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Hello,
Curious to use this resource to try and genotype nuclei in a set of pooled samples of tissues from C57BL/6J mice. Number of samples in each pool ranges from 2-4. Nuclei are reasonably wel…
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Hi! Thanks for all of your work building SICER. It's our peak caller of choice, especially for broad domains!
I occasionally run into an error in the step: "Determining the score threshold from rando…
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There appear to be more command line options in the s/w than you document in the repo. Could you please elaborate on whaat these extra flags do?
~/wgs_resources/bin/TIDDIT.simg TIDDIT.py --sv
…
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Hi,
I have written a tool called pharokka (https://github.com/gbouras13/pharokka) that annotates bacteriophage genomes. Pharokka uses mmseqs2 to match predicted CDS to the PHROGs (https://phrogs.lm…
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Dear developer,
I have installed vdsearch. However, I faced this issue while running $ "vdsearch --help".
Error:
```
Traceback (most recent call last):
File "/home/chong/miniconda3/bin/v…
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Thanks for a great tool and for being on top of open issues - this helped with a lot of trouble shooting.
I now get to an issue I cannot resolve.
I'm running Souporcell with known genotypes:
`/usr/…
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Dear Robert, Jeb and Francisco,
**Describe the issue**
I am working on a plant genome (~500Mb, het=1.29%). As the title mentioned, when I run RepeatModeler, LTR_retriever failed to generate a f…