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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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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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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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