摘要： Ex1: Examine the orchis2 data object. Here you see a two-column data frame with a responsevariable (flower) and a predictor variable (site). Produce a histogram for the sprayed site.Now overlay a density plot.1 ggplot(df, aes(x=value)) + geom_histogram(binwidth=.8, colour="black", fill=&qu 阅读全文

摘要： my $infile = shift;open IN,$infile ||die $!;my @blacklist = qw (chr17_ctg5_hap1 chr4_ctg9_hap1 chr6_apd_hap1 chr6_cox_hap2 chr6_dbb_hap3 chr6_mann_hap4 chr6_mcf_hap5 chr6_qbl_hap6 chr6_ssto_hap7 chrUn_gl000223);while ( <IN> ) { chomp; my $chr = (split /\t/)[0]; if (grep /^$chr$/,@blacklist){ n 阅读全文

摘要： Input is a string of numbers:0012300123400012012311Output will list the none-zero numbers' start and length.Perl语言: 高亮代码由发芽网提供my $nums = shift;my $output = &cluster($nums);print $output . "\n";sub cluster{ my $nums = $_[0]; my @nums = (split //,$nums); my $indicator = 0; my $len = 阅读全文

摘要： % Boxplot coSI exons % Yun YAN % Oct 9, 2012MotivationReproduce the boxplot of the coSI shown in the original paper Figure2 with the graphic tool ggplot.Data SetRaw data is suggested to be formated for friendly usage in R console.Data ProcessingHere I calculate the relative distance to the polyA sit 阅读全文

摘要： MotivationThe ENCODE data comes out, and luckily they provide both.bamfile and.bigwigfile. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool:BEDtoolsand other related tools.ResultI'll first upload the difference between my-version and official version: 阅读全文

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