How to Make Wiggle file from RNA-seq bam

[masylichu]

Hello all,

I use Tophat to align the RNAseq reads to human genome. However, I want to visualize the coverage across the regions of interest.

I know that the IGV can show the wiggles (or bigwig) file.

So, can anyone tell me how to make the wiggle file from the tophat bam file ?

Thanks so much.

[maubp]

There's a Galaxy tool available on the Galaxy Tool Shed bam_to_bigwig which internally calls BEDtools and bedGraphToBigWig, see http://toolshed.g2.bx.psu.edu/

This is a simple Python script (with a Galaxy Tool XML file for use in the Galaxy web GUI), which you can also call directly at the command line.

[masylichu]

Thank you. I have successfully made it.