Last updated: 2018-07-26

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Expand here to see past versions:
    File Version Author Date Message
    html c7f8d14 kevinlkx 2018-07-26 Build site.
    Rmd d6807bd kevinlkx 2018-07-26 add ATAC-seq preprocessing pipeline
    html 64716ac kevinlkx 2018-07-25 Build site.
    Rmd 4e7b89b kevinlkx 2018-07-25 add ATAC-seq preprocessing pipeline
    html 7f2bbe9 Kevin Luo 2018-07-25 Build site.
    html f1b5827 Kevin Luo 2018-07-25 Build site.
    Rmd c8ba1be Kevin Luo 2018-07-25 add ATAC-seq preprocessing pipeline

Step 0: Download JASPAR motif database and install required software tools

JASPAR motif database http://jaspar.genereg.net/download/CORE/JASPAR2018_CORE_non-redundant_pfms_meme.zip

Required softwares:

Step 1: Find TF motif matches using FIMO

sbatch runs on RCC

# match motifs using FIMO ( p-value = 1e-4 ) on RCC

# CTCF MA0139.1
sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/fimo_jaspar_motif_rcc.sh CTCF MA0139.1 1e-4

sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/fimo_jaspar_motif_rcc.sh HIF1A MA1106.1 1e-4

sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/fimo_jaspar_motif_rcc.sh MEF2D MA0773.1 1e-4

Step 2: Get TF candidate binding sites

sbatch runs on RCC


# requires the bigWigAverageOverBed tool from UCSC to compute mapablity
# requires the bedtools to filter out ENCODE blacklist regions

sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/sites_jaspar_motif_rcc.sh CTCF MA0139.1 1e-4

sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/sites_jaspar_motif_rcc.sh HIF1A MA1106.1 1e-4

sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/sites_jaspar_motif_rcc.sh MEF2D MA0773.1 1e-4

Step 3: Count ATAC-seq genome-wide cleavage, and build tagcount bigwig file

sbatch runs on RCC


# bam files
bamfiles=("H1_nomito_rdup.bam" "H2_nomito_rdup.bam" "H3_nomito_rdup.bam" "N1_nomito_rdup.bam" "N2_nomito_rdup.bam" "N3_nomito_rdup.bam")

for bam_name in "${bamfiles[@]}"
do
   echo "${bam_name}"
   sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/genome_coverage_bamToBigwig.sh /project/mstephens/ATAC_DNase/ATAC-seq_Olivia_Gray/ATAC-seq_BAMfiles/"${bam_name}"
done

Step 4: match ATAC-seq tagcount matrices for each motif

sbatch runs on RCC


# bam files
bamfiles=("H1_nomito_rdup.bam" "H2_nomito_rdup.bam" "H3_nomito_rdup.bam" "N1_nomito_rdup.bam" "N2_nomito_rdup.bam" "N3_nomito_rdup.bam")

## CTCF
for bam_name in "${bamfiles[@]}"
do
   echo "${bam_name}"
   sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/get_motif_count_matrices.sh CTCF MA0139.1 "${bam_name}"
done

## HIF1A
for bam_name in "${bamfiles[@]}"
do
   echo "${bam_name}"
   sbatch ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/get_motif_count_matrices.sh HIF1A MA1106.1 "${bam_name}"
done

## MEF2D
for bam_name in "${bamfiles[@]}"
do
   echo "${bam_name}"
   sbatch --mem=30G ~/projects/ATAC-seq/ATAC-seq_workflow/code_RCC/get_motif_count_matrices.sh MEF2D MA0773.1 "${bam_name}"
done

Session information

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.16      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.1.7     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     rmarkdown_1.9     tools_3.4.3      
[16] stringr_1.3.0     yaml_2.1.18       compiler_3.4.3   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1