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Hi team
I know that trimgalore is a wrapper around cutadapt but I want to check what I ran is considered fine
I ran trimgalore to remove adaptors and primers at 5' and 3' ends but then
```
trim…
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[Chen G, Yang X, Ko A, Sun X, Gao M, Zhang Y, Shi A, Mariuzza RA, Weng NP. Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8+ TCR Repertoires to Immunodominant Viral Antige…
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Dear all, thanks for your fantastic work. How can we calculate the beta diversity of unweighted_unifrac, weighted_unifrac from your pipeline?
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It's not clear why this threshold was implemented and what kinds of situations it's supposed to be help with.
It seems like it would accidentally exclude certain kmers from subtype calling if the …
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Thanks for developing this tool for ceDNA analysis. I have some bam files from generated from WGBS data and am wondering if AmpliconSuite is able to use these bam files as input for ceDNA detecion? If…
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Hi there,
I'm very excited to try using `decontam`, but I'm not sure it'll work with our data. I'd be grateful for any advice.
I've got the following `phyloseq` object (16 true samples and 5 con…
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--Hi,
i have simulated 10 CNVs from 100bp to 300 bp (5 gains and 5 losses) on chr20 with SimulateCNVs.py tool , below positions of the simulated CNVs:
chr20 31282724 31283023 6…
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Hi, I am testing crabs to get a reference library of 12S. I noticed that after step 4 I got some small size sequences (for example 20 bps) and in other cases some sequences that bind only by one of th…
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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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### Description of feature
Context in [this Tweet](https://twitter.com/nilshomer/status/1498528699670433795?s=20&t=1uKZpUz-ZkBQKuCobNvyGQ). Used by @peterk87 @fmaguire in [this pre-print](https://www…