09 2012 档案

摘要：Last postintroduced the basic usage of genomeCoverageBed. Here is some update to deal with BAM2WIG processing.As the default output of genomeCoverageBed is formatted as following:chr start depthHowever,WIG file formatis different. The chromosome information is recorded in the header line:variableSte 阅读全文

摘要：Having sequenced and obatain BAM/SAM file, one is going to visulize the data in histogram. WIG, or Bedgraph format file will work. Thus what we need is a tool that convert BAM/SAM file into Bedgraph or WIG file.Before the converting, two things should be prepared.1. BAM file is suggested to be sorte 阅读全文

摘要：I want to plot line graphs to show the y changes along with time series, just like in this post:http://stackoverflow.com/questions/12500218/ggplot2-line-plotting-with-time-series-and-multi-spline/12500368#comment16830065_12500368.However, the x-axis treat the time points as five groups rather than n 阅读全文

摘要：For given RefSeq gene, all reads overlapping with gene are included. (Q1) For given RefSeq gene, only reads overlapping exon are inclued.(Q3) For given Exon, all reads overlapping with exon are inclued.(Q2) 阅读全文

摘要：Questions:could you give an example of intersectBed -split syntax working with the current version of bedtools (v2.16.2)?My input A is a BED12 containing only reads that have been aligned to *exon-exon junctions*.My input B is a gtf annotation file.Since input A contains only reads that have been ma 阅读全文