1、官方流程，太空了，还是得结合文章分析

CUT&Tag Data Processing and Analysis Tutorial

2、paper流程参考

【Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors】

【TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control】

【Genome-wide chromatin accessibility is restricted by ANP32E】

【The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes】

【CSTF2 mediated mRNA N6-methyladenosine modification drives pancreatic ductal adenocarcinoma m6A subtypes】

【Regulation of CTCF loop formation during pancreatic cell differentiation】

paper	fastqc	remove adapter	alignment hg38/mm10	alignment E. coli	remove duplicates	Genomic enrichments	Peaks
Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors	无	无	Bowtie2 parameters: –local –very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700	无	(parameter: REMOVE_DUPLICATES = true) of Picard	deeptools (v3.3.2, parameters bamCoverage –normalizeUsing CPM –binSize 25 –smoothLength 100) and visualized using IGV	MACS2 (parameters: –f BAMPE -g mm –broad)
TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control	无	无	Bowtie2 (--local –very-sensitive-local –no-mixed –no-discordant -I 10 -X 700)	无	PCR duplicates were removed using Picard	tracks were generated using bamCoverageResulting bigwig files were displayed in IGV and heatmaps made with deepTools computeMatrix and plotHeatmap packages	无
Genome-wide chromatin accessibility is restricted by ANP32E	无	无	Bowtie2	无	PCR duplicates were removed using Picard	genome browser tracks in bigwig format were generated from merged replicates using deeptools bamCoverage	MACS2 (setting for H2A.Z ChIP: -f BAMPE–SPMR–nomodel -B–broad; for ATAC-seq: -f BAMPE–SPMR–nomodel -B)
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes	无	adapters were clipped	Bowtie2  with parameters: --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000	mapped to Ensembl masked R64-1-1 with parameters: --end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700.	无	Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v.2.30.0	peaks were called by SEACR (v.1.3) using the norm and relaxed settings
CSTF2 mediated mRNA N6-methyladenosine modification drives pancreatic ductal adenocarcinoma m6A subtypes	FastQC	Adaptor and low-quality bases were removed using Fastp	Bowtie2 with options: -p 6 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700	无	无	Visualization of the depositions along genomic regions was performed with IGV	macs2 callpeak -t input_file -p 1e-5 -f BAMPE –n out_name
Regulation of CTCF loop formation during pancreatic cell differentiation	无	无	Bowtie2 and the hg38 human genome release	无	PCR duplicates were removed using Picard Tools	Normalized reads were used to derive bedgraph files for comparison in IGV.	MACS2 was used to call peaks using default parameters with IgG ChIP-seq data as control