Visualize positive reads upwards, negative reads downwards?

[Di Zhen]

Hi,

I'm new in NGS data analysis. My data is strand-specific single end. I would like to ask is it possible for IGV to visualize positive reads upward, negative reads downward like the question asked here: 

I read the document and notice the option "-strands read" of igvtool to allow counting reads for each strand. I know it's not related to igvtool itself but I still want to ask whether there is a way to modify TDF file by multiplying the counts of reads on negative strand by "-1", so that when uploading the TDF file into IGV I can see positive reads upwards and negative reads downwards? 

If there's any suggestion or help, I'm very appreciated it!!

-Di

[James Robinson]

Hi, you can't do that with igvtools, you would have to do some scripting.   However I wouldn't start from a "TDF" file,  rather a "wig" file, which you can output from igvtools count by using a ".wig" extension from the output file.    Then you could write a script to transform the values to negative.   When complete, make a "bigwig" file with UCSC tools.   This is a basic outline of an approach, but I haven't tried it.

[Di Zhen]

Thank you for your suggestion. That's very helpful!