"chip.ctl_fastqs_rep1_R1" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I1_1.fastq.gz" ], "chip.ctl_fastqs_rep1_R2" : [ "~/project2/analysis/ChIP-seq/encode-pipeline/encc/fastq/ENCC-I1_2.fastq.gz" ], "chip.ctl_fastqs_rep2_R1" : [ "~/project2...
输入文件:~/project/epigenetic/analysis/ChIP-seq/encode-pipeline/encc/H3K27ac/encc.chip.full.json "chip.title":"hENCC ChIP-seq (H3K27ac)","chip.description":"ENCC-K27-2_1,ENCC-I1_1 (1st); ENCC-K27-1_1,ENCC-I2_1 (2st) ","chip.pipeline_type":"histone","chip.aligner":...
一个分析流程是针对ChIP-Seq的,包括转录因子和组蛋白修饰,链接在这里。另一个分析流程是针对ATAC-Seq或者DNAse-Seq的,链接在这里。 之所以说是宝贝,是因为这两个pipeline都提供了一体化的质量控制以及分析流程。开发实验室是我现在所在系的Anshul Kundaje。这两个pipeline也都是我现在老板做的ENCODE的产物。所做的,...
ln: failed to access ‘/home/-/project2/analysis/ATAC-seq/encode-pipeline/encc/subsample/result/atac/a1db1b2f-64b6-4bce-b51b-2d5ee2d316bb/call-idr_ppr/execution/*.bfilt.narrowPeak.bb’: No suchfileor directory ln: failed to access ‘/home/-/project2/analysis/ATAC-seq/encode-pipel...
Design and analysis of ChIP-seq experiments for DNA-binding proteins 发表在nature biotechnology上,网址如下 https://www.nature.com/articles/nbt.1508 在该文章中对chip_seqs数据分析的完整pipeline进行了探究和解释,其中提出了一个peak位点两侧reads分布的规律,如下所示 ...
3.3 Chip-seq 数据分析流程数据分析流程(analysis pipeline)的实现的实现 对于 ChIP-seq 数据分析的质量控制与初步处理,具体流程如图 3-3 所示 图 3-3 Chip-seq 数据分析质量控制与初步处理流程图 3.3.1 参考基因组序列比对参考基因组序列比对 目前有多种序列比对工具(read aligner),但是 Bowtie 是其中最快的而...
eCollection 2015 SepHoules T, Rodier G, Le Cam L, Sardet C, Kirsh O (2015) Description of an optimized ChIP-seq analysis pipeline dedicated to genome wide identification of E4F1 binding sites in primary and transformed MEFs. Genomics data 5:368-370...
CHIP-seq pipeline : http://www.slideshare.net/COST-events/chipseq-data-analysis 大家一定要看这个ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.http://www.ncbi.nlm.nih.gov/pubmed/22955991 编辑校对:思考问题的熊 本站仅提供存储服务,所有内容均由用户发布,如发现有害或侵权...
比如建立一个ChIP-seqtest文件。 在下面建立一系列过程文件夹 mkdir rawdata qc clean align peak 等,相当于一下子建立这么多文件夹。以后每一个步骤都要保存到相应文件夹下。当然也可以现用现建立。 二、可以把不同的分析pipeline所需要的软件打包在不同的环境命令中 ...
Routine ChIP-seq experiments and rigorous bioinformatics analysis are an integral part of Diagenode’s product development and diligent product quality control. In this application note we present our comprehensive analysis pipeline for analyses of ChIP-seq data. We then show a case study where we ...