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Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
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louisflower1999
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Hi GenoMax,
Thanks so much for your suggestion! Those amplicons are around 4.4kb. And there should be at least 1kb from the left and 800 b…
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Wanted to make it a complete answer with an additional command. Moved now.
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Maybe make this an answer rather than a comment?
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You are trying to PCA these by what, exactly? Binned coverage? Is this really informative?
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I don't see a way to specify a random number of accessions to download as an option. Perhaps you may want to open an issue and suggest that…
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@genomax has a good point about trying `pbaa`. The tool will output consensus sequences of the different alleles. You can then use MSA to a…
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Not to get too pedantic but joint genotyping solves a different problem (removing artefactual variants) from producing a population VCF tha…
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Another option would be HAILs VDS Combiner, [https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.V…
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thank you for explanation and documentation
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Illumina sequencing assumes/generally expects that clusters in a sequencing field have an even distribution of ACTG so for every sequencing…
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what do you mean by 'low nucleotide diversity'. If it is low nucleotide diversity, is it supposed to have consistent signals, leading to hi…
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> Does the phred-score is affected by the position of the base in all the reads (vertical), or all the bases that belong to a single read (…
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try glnexus https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
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Thank you so much for you answer @iansudbery! Yes I have read it too and I don't think it's totally clear either, so I guess I might not be…
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