Goal : Find regulatory SNP candidate (rSNP)
Does the SNP impact the sequence affinity with a TF ? (likelihood the TF will bind with this sequence)
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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 ?
- step1:
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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)
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outputs
- TSV file with regulatory variant, and metadata such as TFBS name, score of affinity, impacting score
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Flowchart
