Question: Issue: Scaled Region heat map using Deeptools 2.0 showing no signal, same files and parameters give excellent heat map around TSS.
gravatar for groupelmarwolf
4.0 years ago by
groupelmarwolf0 wrote:

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 -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 -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: blank heat map

Any inputs to who I can fix this issue ?

chip-seq deeptools heat-maps • 1.8k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by groupelmarwolf0

Try removing the --zMin and --zMax arguments and see what happens.

ADD REPLYlink written 4.0 years ago by Devon Ryan98k

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.

ADD REPLYlink written 4.0 years ago by groupelmarwolf0

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).

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Devon Ryan98k
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