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Hi ATpoint,
Thank you for your though provoking answer. Big fans!
Actually I have some normal cells in each sample, and I found good mixt…
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have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
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Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
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Expand your search by searching these (two) sequences against other sets of sequences.
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I'm wondering if this could work:
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What method are you using to identify markers and does it allow for nested designs?
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I will look into this. Thank you!
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example vcf:
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4
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Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
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In general, you should threshold on the p value that corresponds to the maximum FDR you can accept.
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I'm not sure if this will work, but you could use `bcftools view` with [include expressions](https://samtools.github.io/bcftools/bcftools.h…
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