3.1 ATAC-seq分析主要包括3个部分 ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis) # ATAC-seq分析主要由3个部分...
最近在编写全新的ATAC-seq流程,看到一个非常好的文献《From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis》文献堪称是目前最全的ATAC-seq的pipeline教程,对比了很多软件,并给出了结论。笔者总结了一些关键点出来供大家共同学习 摘要 ATAC-seq广泛用于研究染色质生物学的研究,但是该实验得的...
https://github.com/harvardinformatics/ATAC-seqAn ATAC-seq pipeline from Harvard Informatics https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/A similar github page presenting an ATAC-seq pipeline https://galaxyproject.github.io/training-material/topics/epigenetics/...
Wei Z, Zhang W, Fang H, Li Y, Wang X (2018). “esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.” Bioinformatics. doi: 10.1093/bioinformatics/bty141. 出自清华汪小我Lab。哦!对了!DEseq的两个通讯,他是其中之一,另一位是张学工。 你需要做哪些准备? 安装R,安装这个esATA...
Wei Z, Zhang W, Fang H, Li Y, Wang X (2018). “esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.” Bioinformatics. doi: 10.1093/bioinformatics/bty141. 出自清华汪小我Lab。哦!对了!DEseq的两个通讯,他是其中之一,另一位是张学工。
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignmentsdoi:10.1093/nargab/lqab101Jason SmithM Ryan CorcesJin XuNathan C SheffieldCold Spring Harbor Laboratory
补充RNA-seq流程 以前都是自己搭RNA-seq流程,虽然可以完成任务,但是数据量一多,批次多起来,就非常难管理。 既然别人提供了这么好的流程,那就要用起来,管理起来不是一般的轻松。 ENCODE-DCC/rna-seq-pipeline 安装比较麻烦,没有针对local的一键安装,但我们可以借鉴Dockerfile文件里面的安装方法。
alignment can be time consuming, and there is always a trade-off between speed and accuracy. In our experience, the following pipeline performs reasonably well: FastQC➔ trimmomatic➔BWA-MEM➔ATACseqQC, and we would suggest this as a good starting point for processing of ATAC-seq data. ...
bedtools getfasta -fi/home/lizhixin/softwares/miniconda3/share/homer-4.10-0/.//data/genomes/hg38///genome.fa -bed sorted.down.sig.peak.3col.bed -fo sorted.down.sig.peak.3col.fasta intersectBed -a/home/lizhixin/project2/analysis/ATAC-seq/encode-pipeline/ipsc/result/atac/c3097359-919e-...
Unified scATAC-seq data analysis pipeline (PUMATAC) We developed PUMATAC, a unified Nextflow v21.04.3 (ref.29) pipeline, to align samples from multiple technologies to the reference genome and write fragments files from these reference genome alignments (https://github.com/aertslab/PUMATAC). Th...