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 |