computeMatrix & plotProfile for AT% plot

[Anupriya014]

Hi all!
I'm trying to use plotProfile for plotting AT%. For this, I created BED files for upregulated, downregulated & unresponsive genes as region files. For bigwig file, I created bed file for whole genome with interval of 500bp & calculated AT% using 'bedtools nuc' function. This bed file was converted to bigwig file, containing AT% as the values, using couple of tools.

The deeptools commands are here:

computeMatrix reference-point -S /home/whole_genome_sorted_new.bw -R /home/up /home/unresponsive /home/down -a 3000 -b 3000 --referencePoint TSS --outFileName /home/all_matrix_3000_new --averageTypeBins mean --binSize 100

plotProfile -m /home/all_matrix_3000_new -out /home/all_TSS_plot2_new.png --plotTitle "" --yAxisLabel "AT %" --colors red yellow blue --dpi 500 --legendLocation best --plotTitle "" --plotHeight 15 --plotWidth 20

The plot :

But my bigwig file contains data ranging from 0-46 & it's not represented in the plot what can be the possible reason? Please help.

[dpryan79]

Remember that the lines are the average, so it'd be quite surprising for that to be the maximum possible value. For confirmation, you might use plotHeatmap instead, where you're likely to see a few regions with the maximum (or minimum) value.