https://github.com/alleninstitute/graybuck2019analysis

Analysis scripts used for Graybuck, et al. (2019)

https://github.com/alleninstitute/graybuck2019analysis

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Analysis scripts used for Graybuck, et al. (2019)

README.html

graybuck2019analysis
Scripts used for data analysis for Graybuck, et al. (2019).
These scripts are currently available as-is, including references to local files and directories that may not be useful to external users.


Alignment
An example of alignment scripts for a single 50bp paired-end MiSeq run is stored in the alignment_example/ directory.
Parameters for the locations of alignment tools and genomes must be provided in 00_config.sh.
The full alignment procedure as written requires the following tools:

* bowtie: http://bowtie-bio.sourceforge.net/index.shtml

* cutadapt: https://github.com/marcelm/cutadapt/

* trimgalore: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

* samtools: http://www.htslib.org/

* preseq: http://smithlabresearch.org/software/preseq/

* bamToBed: Part of the UCSC kent tools collection http://hgdownload.soe.ucsc.edu/admin/exe/

* Picard Tools: https://broadinstitute.github.io/picard/


scATAC-seq analysis
The primary scATAC-seq analysis pipeline is written in R, and is stored in the gb_analysis directory.
This analysis pipeline requires many R packages, which can be checked and installed with:
gb_cran_reqs <- c("dplyr",
                  "purrr",
                  "ggplot2",
                  "ggbeeswarm",
                  "dbscan",
                  "Rtsne",
                  "data.table",
                  "feather",
                  "Matrix",
                  "matrixStats",
                  "WGCNA",
                  "rbamtools",
                  "BiocManager",
                  "devtools")

missing_cran_reqs <- setdiff(gb_cran_reqs, installed.packages())
install.packages(missing_cran_reqs)

gb_bioc_reqs <- c("GenomicAlignments",
                  "GenomicRanges",
                  "rtracklayer",
                  "limma",
                  "Rsamtools")

missing_bioc_reqs <- setdiff(bg_bioc_reqs, installed.packages())
BiocManager::install(missing_bioc_reqs)

gb_ghub_reqs <- c("AllenInstitute/scrattch.hicat",
                  "AllenInstitute/scrattch.vis",
                  "AllenInstitute/lowcat",
                  "JinmiaoChenLab/Rphenograph")

missing_ghub_reqs <- setdiff(sub(".+/","",gb_ghub_reqs), installed.packages())
devtools::install_github(missing_ghub_reqs)
Separate scripts for joint analysis of data from Graybuck, et al. (2019) and Prefrontal Cortex data from Cusanovich and Hill, et al. (2018) are stored in supp_gb_cu_joint_analysis/.


Level of Support
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.


License
This code is released under the Allen Institute Software License. See file LICENSE for details.


Contributions
Any contributions to this repository are subject to the Allen Institute Contribution Agreement. See file CONTRIBUTING.md for details.

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