How to normalize the bam files for RNA-Seq samples for visualization

Question

[wangdp123]

Hi there,

I would like to compare the visualizations of bam files from different RNA-Seq samples to get a view of the differences among samples. The software would be golden helix software or IGV viewer.

I am wondering if there is a way to normalize the bam files by taking into account the total read number for each sample?

Many thanks,

Tom

Answer 1

[trausch]

Viewing multiple BAM files in IGV is a little slow. We developed Alfred which creates browser tracks and at the same time normalizes to ~30 million reads by default. The resolution parameter '-r' adjusts the file size of the browser track. The default of 0.2 usually results in a browser track of ~150MB in size for RNA-Seq data. igvtools can be used to convert bedGraph files to IGV's preferred tdf format.

alfred tracks -o ucsc.bedGraph.gz input.bam

igvtools totdf ucsc.bedGraph.gz igv.tdf hg19