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I am running CNVkit using two options. First, I am using three samples as a reference and second, I am running it without any reference. However, in each case, the sex identified is opposite. How to d…
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In order to connect datasets with their associated interaction claims, we'd like to use elton nanopubs as a started point to create a dervied web annotation snippet.
The goal is to identify additi…
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Observed in maptest.ucsd.edu against qiita-rc db: Usually computing pool values for a single plate works fine, but occasionally for a single plate, and reliably if more than one (96-well) plate is add…
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Dear,
I am leaving the Nanopore Day in Bordeaux and there Stephen Rudd presented the release of this promising tools.
What should be the size of the training set? Number of reads of the same ref…
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Hi,
I confused in a topic about the CNVkit algorithm.
![image](https://user-images.githubusercontent.com/60985581/123441741-de0f5400-d5dc-11eb-9425-0a5d8b073aae.png)
This picure came from cn…
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We're currently adding all alignments into the ARG regardless of how much missingness there is. We currently have a max_masked_sites_per_sample of 6535 (2021-02-26) which seems quite high.
What wou…
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Hello!
I am using cutadapt to demultiplex my reads (v2.10 with Python 3.7.6).
Basically, I have a pair of fastq files (e.g. input_R1_001.fastq and input_R2_001.fastq) which contain sequences fro…
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We have lots of reversions, but beyond "immediate" reversions (those reverting a mutation on the parent node), it's not clear how to identify them. One clear way might be to look at mutations that hav…
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I have been running `wf-clone-validation` in Google Cloud Batch but I've been observing a linear relationship between the number of samples and the time taken to run everything. My assumption was that…
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Hi, everyone!
I'm trying to import my tsv files generated by PICRUSt2 into ggpicrust2 and the program adds an "X" before the name of my variables and then I can't run the metacyc_daa_results_df bec…