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Question: Normalization when convert bam to wig
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gravatar for rongruo1988
2.5 years ago by
rongruo1988 • 0
rongruo1988 • 0 wrote:

Hello, I am new to the bioinformatics analysis, I want to display bam coverage in IGV to show the gene expression level, I'd like to know how to convert bam to wig or bigwig in Galaxy, and if normalization is needed when convert to wig file for each sample, and which normalization method to use? and also if normalization is needed between different samples when display the wig file in IGV(i.e. Do I need to normalize the tracks in IGV when display multiple tracks at the same time?) Is there any paper published with detailed protocol for such analysis and display? Thanks for the help!
rna-seq galaxy samtools bam • 1.8k views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by rongruo1988 • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Most visualization browsers offer options that will summarize depth of coverage (IGV, UCSC, Galaxy). From detailed lists to one-line heatmaps.

Some tools require compressed input, you could use: Convert, Merge, Randomize BAM datasets -> Convert Bam to Bed.

Tools in BEDTools and RNA-seq can perform data reduction with certain tools and others can compare samples. If the summarized data output is in Wig or Bedgraph format, then it can be converted with Wig/BedGraph-to-bigWig converter.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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