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Hi, I would like to run MAGinator on a pretty large data set. I have around 420 samples, with 60 bins per sample on average, and the preprocessed reads are around 6GB each sample.
I have been runn…
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Hi @ctb the sourmash author,
Currently we are working on using your tool to find the representative MAGs within a customed data set assembled from several deeply sequenced stool shotgun samples. Th…
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Hello,
Do you think it is possible to use LDna on a large number of SNPs (>1 000 000) obtained through Whole-genome sequencing? If so what would you recommend to build the LD matrix?
Thanks
Claire
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Could you please provide the following information:
1. example syntax for DNA_FT.py
2. example input and output file pair
3. list of dependencies for installation (preferably using downloads all …
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I produced nested PRGs (`--min_match_length`=7, `--max_nesting`=5) from multiple sequence alignments of plasmodium genes and found that `make_prg` can produce ambiguous PRGs.
Here's an example I…
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```
What steps will reproduce the problem?
1. Open AltAnalyze and begin
2. Click on Add New Species
3. receive error and program crashes
What is the expected output? What do you see instead?
Wha…
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Dear all,
I ran the test files and work perfectly. When I ran my own data, I have a problem with the Strain clustering and assembly step. I have this problem
*** End window construction
Invalid…
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Hi Isaac,
I'm running ipyrad [v.0.9.90] with maximum memory allocation (184G), 48 threads, and with the following (relevant) params:
```
~/all_trimmed_reads/*.fq ## [4] [s…
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Hello,
I am experimenting with different tools for transcriptome assembly on a data set of RNA-seq reads from tomato I obtained from SRA. I used StringTie to assemble the transcriptome and then ran…
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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…