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Recent Replies
Answer: Differential binding analysis between different TFs
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have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
also, I am not sure how you can compare different TFs, the…
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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.
That said, why does it feel like this is an [XY pro…
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I'm wondering if this could work:
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You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
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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!
Comment: count number of polymorphic sites among samples in vcf
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example vcf:
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chr1 100 . C …
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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 guess reference-based annotation is not an option?
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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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> However, I want to exclude sites where all of the individuals have a single alternative allele (or a mix of either one alternative allele…
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