MEMOS

Mutation Enrichment of Motifs

Developed by Parisa Mazrooei and Tahmid Mehdi MEMOS has been used for the analysis of Mazrooei, Parisa, et al. "Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors." Cancer cell 36.6 (2019): 674-689.

Description

MEMOS computes the enrichment of mutations within motifs and flanking regions of your transcription factor of interest.

Location on the cluster: /mnt/work1/users/lupiengroup/CommonScripts/MEMOS-wrapper/

Installation

Download the repo via git clone.

Usage

sh memos-pipeline.sh TF FASTA MUT N_PERM OUTDIR PVAL FLANK BED

Parameters

Parameter	Description
TF	Name of your transcription factor of interest. This name will be used to lookup the motif for that transcription factor
FASTA	FASTA file containing the regions to be scanned
MUT	VCF file of mutations
N_PERM	Numer of permutations for permutation test
OUTDIR	Output directory
PVAL	P-value for permutation test. 0.001 recommended
FLANK	Length of flanking region. This will be considered for both left and right flanking regions
BED	Optional. Background regions for permutation test. If not provided the whole genome is the default

Notes

1. All paths given should be absolute paths
2. At the moment, VCFs are considered to match 1000GenomeProject format which means Chromosomes are considered without chr at the beginning of the chromosome number