README.md

Work record in David lab(2019.7.30-2019.8.25)

Ⅰ. Single-cell RNA-seq analysis

Day2 single-cell RNA-seq analysis: Seurat package

1. batch effect assessment

Script : "single-cell-RNA-batch.r

2. Clustering

Scripts : single_cell_cluster.r

Ⅱ. Heatmap of differential expression genes in important pathways

1. search differential expression genes in some pathways

(1) Using R package to get pathways' genes.

Geting pathway's KO number: https://www.genome.jp/kegg/pathway.html Script : ko_pathway_genes.r

(2) Search genes in KEGG enrichment analysis's results

(3) Switch "gene ID" to "gene name"

Script : ID_simbol_genename.r

(4) CPM count matrix

pathway_gene.xlsx

(5) Fig. Heatmap

heatmap.r

Ⅲ. Heatmap of migrasome associated genes

Yu Li Lab migrasome associated gene list's heatmap

(1) Script : migrasome_heatmap.r

(2) analysis : email

Ⅳ. paper's profile (Fig.5)

(1) klf5/Foxa2 dependent and repress's ChIP-seq/ATAC-seq data's heatmap

Script : ChIp_heatmap.sh

(2) klf5/Foxa2 dependent and repress's ATAC-seq profile

Script : profile.r

Ⅴ. profile of GAIN region in our ATAC-seq/Kras ChIP data

(1) Switch mm9 to mm10

a. Using UCSC tools b. Using CrossMap software

(2) overlap ragion's computeMatrix

Script : computeMatrix.sh

(3) profile

Script : the same as profile.r

Ⅵ. TF overlap Venn Fig

(1) cat all factors together

Script : extract_peaks.sh

(2) Venn Fig

Script : venn.r

Ⅶ. upload bigwig file to UCSC browser

(1) load bigwig data to a network to get a URL link

the network is : https://de.cyverse.org/de/

(1) load data to UCSC gene browser

Annotation file : uscs.txt