IGV cannot see heatmap of SEG file · Biostar

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IGV cannot see heatmap of SEG file

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

• 3,017 views • link

updated 4.6 years ago by Ram

• written 11.9 years ago by xiaoyonf •

1 answer

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

• 0 views • link

updated 4.6 years ago by Ram

• written 11.9 years ago by xiaoyonf •

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