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Source code for RNA-seq and ATAC-seq results presented in Dhara et al. (2019)
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1_preprocessing
2_differential-analysis
3_peak-gene_annotation
misc
.gitignore
README.md

README.md

Source code for Dhara et al. (2019)

This repository contains the following source code files used to analyze the RNA-seq and ATAC-seq data in Dhara et al. (2019).

It is organized as follows:

  • 1_preprocessing/

    • ATACseq

      • 1_merge_lanes.txt: concatenate sequencing lanes containing technical replicates into a single file
      • 2_trimgalore.sh: trim adaptor sequences
      • 3_fastqc.sh: validate sequence quality
      • 4_bwa_alignment_danio_w_transgene.sh: align reads to the zebrafish genome (GRCz10) and transgene sequence
      • 5_fastqc_aligned.sh: validate aligned sequence quality
      • 6_macs_peaklets_alltimes.sh: call peaks from aligned reads and identify summits of deconvoluted subpeaks were identified
      • 7_remove_MTduplicates.sh: remove duplicates and multiple mapped reads
      • get_fasta_from_bed.sh: script to obtain fasta file of sequence corresponding to a provided bed file
    • RNAseq

      • 1_trimgalore.sh: trim adaptor sequences
      • 2_fastqc.sh: validate sequence quality
      • 3_kallisto_hdf5.sh: quantify transcriptome abundances using HDF5 data format
  • 2_differential-analysis/

    • ATACseq

      • 1_differential-analysis_diffBind_all-vs-0.R: perform differential analysis of quantified peaklets for time points 2, 4, 7, and 12 versus 0 using diffBind
      • 2_sigresults-as-bed-file.R: output bed files of significant peaks
      • 4timepts_vs0_results/: folder containing result files (bed and csv) for each comparison
    • RNAseq

      • 0_my_sleuth_functions.R: internal function slightly modifying the sleuth code to enable target IDs to be updated
      • 1_differential-analysis_sleuth.R: perform differential analysis of expression data for time points 2, 4, 7, and 12 versus 0 using sleuth
      • 4timepts_vs0_results: folder containing result files (csv) for each comparison
      • format_kallisto_as_pseudosam/: folder containing helper scripts to convert kallisto quantifications to a pseudosam file for visualization in IGV
  • 3_peak-gene-annotation/

    • 1_make_MEME_format.R: script to automate making a file in MEME format based on Jaspar and Lambert IDs
    • 2_AME_reformat.R: script to reformat AME results for downstream analysis
    • 3_TF_cooccurrence-graphs.R: produce visualizations of TF motif co-occurrence (network plots, UpsetR plots, bar graphs, heatmaps)
    • 4_identify_distal-proximal_peaks.R: identify annotations for peaks (e.g. distal and proximal to genes, exonic/intronic/overlapping TSS)
    • peaklets/: folder containing MACS output files for peaks (ATAC.nodup.unique.macs.peaklets_peaks.narrowPeak) and peak summits (ATAC.nodup.unique.macs.peaklets_summits.bed) as well as a bed file of peaklet locations (ALLMERGED_ATAC.nodup.unique.macs.peaklets_peaks.pvalsort.narrowPeak_500bp.bed)
  • misc/

    • checking_final_numbers.R: script to check final numbers for the paper
    • danRer10_alias.tab: alias file providing correspondence between UCSC and Ensembl chromosome naming schemes
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