Expression levels in IGV

Question

[aylin.cesur]

Hello All,

I have the outputs of analyzing whole genome of human and mouse in SB Genomics, but I could not find out the expression levels of some specific genes in IGV because the files do not have extension of "res". What can I do to find the expression levels of genes in IGV? Thank you for your considerations.

Sincerely

Aylin

Answer 1

[Malcolm.Cook]

Take a look at IGV's support for .tab files, in which rows are genes (or probes) and columns are samples/experiments. What does SB give you? I know they have many different "tasks", so it will depend on that. Cufflinks FPKMs? HTSeq read-counts? In either case, convert your SB data to that format, possibly with additional conversion to column-wise z-scores (i.e. use scale in R, if you know how). That will visualize nicely in IGV. You will need an IGV genome whose gene names are the same as the ones used in the SB analysis.

Answer 2

[aylin.cesur]

First of all, thank you so much for your reply. Yes, I have outputs of cufflinks FPKMs as txt file. Yet, I don't know how to convert to that format.