Lift genome positions Genome positions are best represented in BED format. UCSC provides tools to convert BED file from one genome assembly to another. Binary liftOver tool We need liftOver binary from UCSC and hg18 to hg 19 chain file. Provide BED f…

First step, installation: download from UCSC genome browser chmod + x Second, very important: to download the "Chain File". What is "chain file"?  --- to transfer the gene data from one build to another . for example, from hg19 to hg18…

Reference Genome Components 1. GRCh38 is special because it has alternate contigs that represent population haplotypes. Don't know alternate contig from alternate dimension? Spend five minutes now to review terminology in our Dictionary entryReferenc…

今天要讲的一篇是发表于 Hum Genet 的 "Shared genetic architecture between metabolic traits and Alzheimer's disease: a large-scale genome-wide cross-trait analysis" .很中规中矩的一篇文章,没有什么大的亮点的.写它的主要原因整篇文献思路很流畅,次要原因是我懒,不愿意看费脑子的文章. 以下,进入主题: 背景 阿尔茨海默病(AD)是一种进行性和破坏性的神经…

http://homer.salk.edu/homer/ [怪毛匠子-整理] 使用HOMER分析CLIP-SEQ数据 24 5 2月 2013   | 程序员 Tags: 生物信息学 · 软件 HOMER是一个使用perl和C写成的motif分析工具.之前在分析clip-seq分析时,按照文献中材料和方法所写的流程进行分析,却无法得到与文献一致的结果.想来多半是文章发表时,并没有把所有的细节写清楚,导致我在重复时参数选择方面并没有与原作者保持一致.另一个原因是基因组几经修改,原本的hg17的数据…

From: https://arnaudceol.wordpress.com/2014/09/18/chromosome-coordinate-systems-0-based-1-based/ I’ve had hard time figuring out that different website and file formats are using different systems to represent genome coordinate. Basically, the bases…

  circRNA数据库的建立 wget http://circbase.org/download/human_hg19_circRNAs_putative_spliced_sequence.fa.gz gunzip human_hg19_circRNAs_putative_spliced_sequence.fa.gz wget http://circbase.org/download/mouse_mm9_circRNAs_putative_spliced_sequence.fa.gz gunz…