This repository contains the source code for the sequence analysis.
Please refer to files in ref_file/. Required files are listed in each script.
Primary analysis for RNA-seq was performed using script bellow.
- RNA-seq ->
1_HFF-1_in_house_RNAseq_analysis.sh
Primary analysis for ATAC-seq and ChIP-seq were performed using an established pipeline.
- ATAC-seq ->
2_HFF-1_in_house_ATACseq_analysis.sh - ChIP-seq ->
3_HFF-1_in_house_ChIPseq_analysis.sh
Ubuntu version 20.04
| Package Name | Version |
|---|---|
| Trim Galore! | 0.6.6 |
| hisat2 | 2.2.1 |
| Samtools | 1.9 |
| Subread | 2.0.1 |
| BEDTools | 2.30.0 |
| HOMER | 4.11 |
R version 4.2.1
| Package Name | Version |
|---|---|
| DoRothEA | 1.8.0 |
| clusterProfiler | 4.4.4 |
| DESeq2 | 1.36.0 |
| ChIPseeker | 1.32.1 |
| rrcov | 1.5.2 |
To reproduce results, please perform the analysis in the following order.
1_HFF-1_in_house_RNAseq_analysis.sh2_HFF-1_in_house_ATACseq_analysis.sh3_HFF-1_in_house_ChIPseq_analysis.sh4_Transcription_factor_enrichment.R5_Gain_peaks_ATAC_ChIP_seq.R6_Motif_enrichment_ATAC.sh7_Differential_peak_ATAC_ChIP.sh8_Gene_annotation_differential_peak_ATAC_ChIP.R9_public_RNAseq_analysis.sh10_heatmap_correlation_invivo_invitro.R11_RNA_ATAC_Con_vs_TGF_THBS1_FMOD.R12_VennTest.Rmd