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ltr7yprojectanalysis's Introduction

LTR7Y Project Analysis

Scripts for bioinfomatics analysis of LTR7Y project.

Summary:

01preprocess
File Description
Preprocess_ATACseq.sh Preprocess of ATAC-seq data, including QC, trimming, alignment, peak calling
Preprocess_CutTag.sh Preprocess of Cut&Tag data, including QC, trimming, alignment, peak calling
Preprocess_ChIPseq.sh Preprocess of ChIP-seq data, including QC, trimming, alignment, peak calling
Preprocess_RNAseq.sh Preprocess of RNA-seq data, including QC, trimming, alignment, quantification
Preprocess_scRNAseq.sh Preprocess of scRNA-seq data, including QC, trimming, alignment, quantification
02downstreamanalysis
File Destription
DEG.R Differential expressed genes
DETE.R Differential expressed TEs
Barplot_DETEpct.R Barplot of top DETE percentage
Heatmap_expression.R Heatmap of gene/TE expression pattern
PCA.R PCA plot of KLF5 KOs
scRNAseq_analysis.R naive hESC scRNA-seq downstream analysis
Heatmap_signalenrichment.sh Heatmap of TF/histone/motif signals over TEs or peak regions

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