IGV cannot see heatmap of SEG file

Question

[xiaoyonf]

Hi, I have problem to use IGV tool. I am pretty new to IGV, so please help me!

I produced a SEG file using whole-genome Nimblegene array data (125k) which only including a region of chr14 (~200kb). I opened it in IGV under hg18 but can't see anything the aligned heatmap. But I can see the heatmap under hg19, which I assume I can't use it as a ref, since this array is using hg18.

Please help me, I am really interested in the CNA in this region...

Thanks,
Xiaoyong

Answer 1

[xiaoyonf]

OK, I solved my own problem. Somehow the IGV can not accept "chr14" string under hg18 in the chromosome column. When I changed them into numeric 14, and reload the SEG file, I can see the heatmap!

Thanks,
Xiaoyong