open_chromatin
This is the repositiory the for paper entitled:
Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia
Published manuscript: To be updated soon
bioRxiv version: https://doi.org/10.1101/427484
Note: There were substantial changes betweent the preprint and published versions.
Most data processed and used by code in this repo is deposited on Zenodo (Concept DOI):
Please contact me at phook2 [at] jhmi.edu with any questions or comments.
April 2020
Supplemental_Code_1 for Hook and McCallion, 2020
- align_peak-calling: Contains code pertaining to the alignment of ATAC-seq reads, the calling of open chromatin peaks, and the visualization of this data
- annotations: Contains code pertaining to processing of promoter-capture Hi-C data and VISTA Enhancer Browser data
- fine-mapping: Contains code pertaining to the set-up, execution, and analysis of fine-mapping of schizophrenia SNPs
- jaccard_comparisons Contains code pertaining to the download of Roadmap Epigenomics Project open chromatin data and the base pair level pairwise comparisons performed in the manuscript
- ldsc: Contains code pertaining to the set-up, execution, and analysis of heritability enrichment analyses performed with LDSC using mouse-derived human open chromatin profiles
- ldsc_peaksets: Contains code pertaining to the set-up, execution, and analysis of heritability enrichment analyses performed with LDSC using subsets of mouse-derived human open chromatin profiles. Some code used for this analysis will be in the "ldsc/" directory
- liftover: Contains code pertaining to the conversion of mouse open chromatin profiles to human open chromtain profiles
- peak_comparisons: Contains code pertaining to the peak level comparisons of mouse-derived human open chromatin profiles and human open chromatin profiles
- sc_read_extraction: Contains code and some key files pertaining to the extraction of single-nuclei ATAC-seq reads belonging to clusters of cell populations from "Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation" (Preissl, 2018)
Note: More details for all the scripts within each folder is provided by the README.md in each folder
Data can be found here on Zenodo here with the prefix "gr_": https://doi.org/10.5281/zenodo.3253180
Previous updates
09-04-2019
Major code update! All code added and updated for the second version of the manuscript posted on bioRxiv above. Each directory contains a README.md document in which I have provided detailed descriptions of all code in the directory.
06-26-2019
Added a bunch of code including code using in ATAC-seq alignment and peak calling (align_peak-calling), linkage disequilibrium score regression (ldsc), liftOver (liftover), comparison of peaks (peak_comparisons), read extraction from single-cell data (sc_read_extraction), and fine-mapping of SZ loci using PAINTOR (fine-mapping).
06-14-2019
As will surely be obvious, this repo was not continuously updated!
A new manuscript with modifed and additional analyses is nearing completion so the smattering of code associated with v1 of the manuscript is now archived in the "v1_archive" directory.
New scripts will be uploaded for the new manuscript shortly! Stay tuned!
10-15-2018
- Added output from "ldsc_R_code.Rmd" including figures 1, 2, S2, and S3
10-10-2018
- Uploaded code for running LDSC on ATAC-seq peaks ("running-ldsc.md")
- Uploaded BED file ("hg19_combined_peaks.tar.gz") containing all peaks used in LDSC analysis. This includes chromosome, start, end, and cell population where the peak came from.
- Uploaded BED file ("mm10_merged_peaks.tar.gz") containing the mm10 merged peak set. This includes chromosome, start, end, and number of cell populations from which the merged became came from.
- Uploaded RMarkdown used to visualize and further analyze LDSC results ("ldsc_R_code.Rmd"). Files produced by this script are also slowly being added to the repo.
10-01-2018
- Results and logs from LDSC cell type specific analyses ("ldsc_cts_results" and "ldsc_cts_logs", respectively) have been uploaded
- Logs from LDSC summary statistic munging ("ldsc_sumstats_logs") have been uploaded