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Hello,
I am trying to trim the primer off of 16S Miseq reads ( I am using just 4 samples, 8 fastq PE files as a toy dataset ) and I am having trouble understanding how the `removePrimers` function w…
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Dear Canu Team,
I have recently compiled a more recent version of Canu (-- canu snapshot v2.3-development +162 changes (r10433 c61ebbb7a5f90abb9c034650e2fd95642138de31) to assemble small amplicons…
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I uploaded the [example data](https://github.com/loculus-project/example_data/tree/main/ebola_zaire) for ebola zaire (which we may be out of date) and found preprocessing stalled. When looking at the …
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Hi all,
I'm relatively new to async Rust, but I noticed noodles has async readers and writers and figured I'd give them a shot for one of my projects. I'd like to asynchronously read compressed FAS…
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Hi!
I have demultiplexed sequences for eukaryotes (18S) and bacteria (16S) in the same fasta file. I would like to analyze only the sequences for bacteria. I was wondering if I should separate them b…
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Hello,
I am using Clair3 for variant calling on amplicon sequencing data from a minION, generally with a fair amount of success. However, for one particular amplicon, I get a large number of false ne…
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Dear developer, can you please explain a little bit the algorithm and idea behind normalization in normalizeCNV()?
I have not found in publication an explanation of the method.
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Hi,
I keep getting this error.
I still end up with files in the output, but it looks like the script is trying to generate a strange output directory path.
The output set for this run was 'ampl…
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Hi,
I have an experiment wih a whitelist composed of 35 barcodes (60bp long, non standard technology in development) and when I try to run bustools correct I immediately obtain :
(/bioinfo/local…