rimanb / chem-map

This repository collect scripts and general code used for the analysis of Chem-map datasets

[Read processing] (./bash_commands_deeptools.sh)

bash, python and R scripts used for different part of the data processing

Raw G4 signal of bulk cells at consensus G4 regions

Raw G4 signal of single cells and bulk samples at consensus G4 regions

Characterisation of single cells clusters base on G4 loci homogeneity

fold enrichments at genomic loci of all G4 loci and of top 25% observed G4 loci

structural characterisation of all G4 loci and of top 25% observed G4 loci

Software, tools and environment used demuxIllumina version 3.0.9 FastQC v0.11.8 MultiQC v1.11 cutadapt bwa 0.7.17-r1188 Picard version 2.20.3 (Picard MarkDuplicates) Seacr version 1.3 deepTools version 2.0 bedtools v.2.30.0 DiffBind version 3.15

Cite Chem-map Zutao Yu, Jochen Spiegel, Larry Melidis, Winnie W. I. Hui, Xiaoyun Zhang, Antanas Radzevičius, Shankar Balasubramanian. Chem-map profiles drug binding to chromatin in cells. Nat. Biotechn. In press