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I try to remove duplicates (up to 2 mismatches) from the example below running:
cd-hit-dup -i input.fa -o output.fa -e 2
cd-hit-dup retrieves 8 clusters, when it should be 2 clusters: A and B. Only p…
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Add a warning that -*-protocol options and seq_type differ (at least for tumour). To ensure seqtype WXS doesn't get WGS as SAMPLE protocol set in the VCF.
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**Describe the parameter code you need**
Metabarcoding datasets usually come with relative abundances in terms of sequence reads per ASV or OTU. This is a request for terms for:
- Total abundanc…
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Dear,
I am running CNVkit to call cnvs on samples sequenced with WES sequencing, and get an error below:
`Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Traceback (mo…
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Hello,
I was wondering if you knew of any good publicly available datasets for the V3 Artic Tiling Amplicon sequencing of hCoV-19. Ideally I would love to have a test dataset showing each of the v…
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Different but interesting alternative synthetic controls:
> Wilson *et al.* (2016) Recognizing false positives: synthetic oligonucleotide controls for environmental DNA surveillance.
> https://doi…
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Hi, I am trying to use octopus for liquid biopsy samples. In this context I have deep (10,000x) targeted (~1.3Mb Panel) sequencing data which are preprocessed by deduplication and bqsr (gatk). So cove…