Allele-Specific Analysis of Codebook ChIP-Seq and GHT-SELEX data

This repository contains the results of allele-specific analysis of Codebook ChIP-Seq and GHT-SELEX data, see [https://doi.org/10.1101/2024.11.11.622097] for details.

Files and contents

SNP_calls_filtered_chipseq.tar

SNP_calls_filtered_selex.tar

The tar archives contain gzipped VCF files (one per transcription factor and read alignment, separately for ChIP-Seq and individual GHT-SELEX cycles) with the SNP calls obtained from Codebook data. The files were filtered to include only candidate ASBs (allele-specific binding sites): common SNPs with dbSNP rsIDs with both Ref and Alt alleles supported by 5 or more reads. Triallelic SNPs are split into biallelic records.

ASB_calls_annotated_chipseq.zip

ASB_calls_annotated_selex.zip

The zip archives contain tsv tables (one per transcription factor) with the results of MIXALIME ASB analysis and PERFECTOS-APE motif annotation.

* Please refer to [https://doi.org/10.1101/2024.11.11.622097] and [https://github.com/autosome-ru/mixalime/] for technical details regarding the contents and designation of individual table columns of the *.tsv files and the technical details of the SNP calling and ASB analysis.