custom BED files for heatmap

[seba...@gmail.com]

hi all

i have a bed file containing only chr #, start, end positions for some intervals from ChIP Seq data.

i downloaded your TSS file for hg.19 and loaded it correctly...i'm able to visualize under "Merged dataset profile" what (i think) it's the mean density around the TSS for my file..but if i look at the heatmap i only see a red (or whatever color i choose) block.

furthermore, if i look at "Density values" i only see 0's all the way through and i can't get a real heatmap.

my steps were:

1) go in Density Array Method

2) load the TSS file

3) load my bed file

4) "Load file(s)"

5) Extract Data

6) right click on the data create in "Step 3: clustering -- Distribution List" and choose "visualization on Heatmap"

6a) if i use "clustering" with KMeans raw, i do get a few clusters with peaks in the "Merged dataset profile" but i don't get any heatmap (only a red box)..

...any suggestions?!

thanks

[Tao]

Hi,

you need to load a real raw chipseq read file in bed or bam format, not only a interval file.

Tao