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Add sneep (Nina Baumgarten et al) to investigate if a SNP is probably destroying a TF motif #65

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Firestar93 opened this issue Oct 19, 2023 · 3 comments
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enhancement New feature or request question Further information is requested

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@Firestar93
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@nictru nictru added the enhancement New feature or request label Oct 19, 2023
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nictru commented Oct 19, 2023

Requires #61 to be finished first

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nictru commented Oct 21, 2023

I assume the workflow will look approximately like this:

  1. Identify motif regions based on STARE input regions using FIMO (Prepare FIMO script #61)
  2. Fetch VCF file containing all known SNPs for a given genome
  3. Intersect motif regions with SNPs
  4. Use remaining SNPs as input for Sneep
  5. Include the Sneep output to the report

Is this approximately what you imagined @Firestar93 ?

@nictru nictru added the question Further information is requested label Oct 22, 2023
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Yes, just that the regions that we search with FIMO are only predicted and prioritized enhancers and promoters from STARE not all regions. Also: in these enhancer and promoter regions we only search for motifs with FIMO for TFs that were prioritized.

@nictru nictru assigned LeonHafner and unassigned nictru Oct 26, 2023
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