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Puriney's Notes

Puriney=purine+Y, my Wonderland

 
 
 

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[bio-tips] genomeCoverageBed introduction  

2012-09-24 11:33:38|  分类: Bio |  标签: |举报 |字号 订阅

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Having sequenced and obtained BAM/SAM file, one is going to visualize 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 sorted with SAMTOOLS. The input is `mapped.bam`, and out sorted file is `sort.mapped.bam`

samtools sort mapped.bam sort.mapped.bam

2. chromInfo file is needed. 

chromInfo file records the length for each chromatin. And can be available from UCSC genome browser. 

#chrom    size     
chr1    197195432 
chr2    181748087 
chr3    159599783 
chr4    155630120

[bio-tips] genomeCoverageBed introduction - Puriney - Purineys Notes
 

Next, let's hit it. 

1. BAM2Bedgraph

genomeCoverageBed -bg -ibam sort.mapped.bam -g genome.chromInfo >genomewide.bedgraph

2. BAM2Wig

genomeCoverageBed -d -strand + -ibam sort.mapped.bam -g genome.chromInfo >genomewide.wig

Calculating the forward strand coverage. And Wig file is 1-based coordinated format, thus we use the -d option. 


====

More details are available in the help document. 



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