Entering edit mode
7.2 years ago
groupelmarwolf
•
0
I tried to create a heat map using computeMatrix reference-point which gave excellent result:
computeMatrix reference-point -a 2500 -b 2500 -bs 5 -p max --sortRegions no -R /home/Data/reference/RefSeq_All.BED -S loucy_input_sorted.bw -out input_sorted_loucy_wg.txt.gz
plotHeatmap -m input_sorted_loucy_wg.txt.gz \
-out input_sorted_loucy_wg.png \
--colorList white,blue \
--zMin 0 --zMax 5
However, when using the same inputs/parameters for computeMatrix scale-region, the resulting heat map is blank.
computeMatrix scale-regions --regionBodyLength 1500 -a 500 -b 500 -bs 10 -p max --sortRegions no -R /home/Data/reference/RefSeq_All.BED -S loucy_input_sorted.bw -out input_sorted_loucy_SR.txt.gz
plotHeatmap -m input_sorted_loucy_SR.txt.gz \
-out input_sorted_loucy_SR.png \
--colorList white,blue \
--zMin 0 --zMax 5
The blank heat map is like this:http://imgur.com/ByJIYr7
Any inputs to who I can fix this issue ?
Try removing the
--zMin
and--zMax
arguments and see what happens.Nothing. It gives me the same output.
But when I give smaller regionBodyLength, it works.
Maybe I should have played around a bit more before posting :/
Thanks for super quick response.
Weird, it should not be all black either way. The output from computeMatrix is a gzipped text file. For the cases where the heatmap is black it'd be interesting to see what the values in a few lines are (the first 6 columns are basically BED file columns, so look after that).