search

daisybio / TF-Prioritizer

Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data
GNU General Public License v3.0
13 stars 0 forks source link

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

Open Firestar93 opened 10 months ago

nictru commented 10 months ago

Requires #61 to be finished first

nictru commented 10 months ago

I assume the workflow will look approximately like this:

  1. Identify motif regions based on STARE input regions using FIMO (#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 ?

Firestar93 commented 10 months ago

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.