Question: IGV cannot see heatmap of SEG file
0
gravatar for xiaoyonf
4.7 years ago by
xiaoyonf10
Baylor College of Medicine, Houston, Texas, USA
xiaoyonf10 wrote:

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

igv alignment • 1.3k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by xiaoyonf10
1
gravatar for xiaoyonf
4.7 years ago by
xiaoyonf10
Baylor College of Medicine, Houston, Texas, USA
xiaoyonf10 wrote:

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

ADD COMMENTlink written 4.7 years ago by xiaoyonf10
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