This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to normalize the bam files for RNA-Seq samples for visualization

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

rna-seq normalization visualize
• 3,068 views • link
updated by trausch trausch • written by wangdp123 wangdp123

1 answer

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
• 1 views • link
written by trausch trausch

Log in to answer this question.

More posts like this