chklopp/hackathon_nextflow_nov2020

Hackathon_NextFlow_Nov2020

Goal : Find regulatory SNP candidate (rSNP)

Does the SNP impact the sequence affinity with a TF ? (likelihood the TF will bind with this sequence)

• Principle

  • step1:
    We expect to find rSNP candidate in a 2kb window upstream of TSS start. We filter the SNP file, keeping only the corresponding SNP.
  • step2:
    For each filtered SNP, we create ref and alt sequences correponding to SNP ref and alt base and its surrounding sequences (+/- 14bp)
  • step3:
    We download the matrices from existing database (TRANSFAC,JASPAR, HOCOMOCO) and prepare them (PWM <-> PFM, ratio, distrib)
  • step4:
    For each filtered SNP, we compare the ref and alt sequences to each TF matrices
    Does ref and/or alt sequence have a strong affinity with TF (putative TFBS)?
    Does the SNP impact the putative TFBS ?

• inputs

  • Genome reference file: Fasta and annotation in GTF file
  • Variant file : in VCF format
  • TFBS pattern matrices : directory of PWM files (one file per TFBS)

• outputs

  • TSV file with regulatory variant, and metadata such as TFBS name, score of affinity, impacting score

• Flowchart