Question: Deeptools - ComputeMatrix: Why does 'referencePoint center' gives the same heatmap as 'referencePoint TSS'
0
gravatar for salamandra
9 months ago by
salamandra180
salamandra180 wrote:

Why am getting exakly the same heatmap when using as reference Point the center of the peak or the TSS of the peak with 'Deeptools ComputeMatrix'?

With 'center':

 computeMatrix reference-point -S file_4heatmap.bw -R file_peaks_sorted_clip.bed -out file_matrixcenter.gz --referencePoint center --outFileSortedRegions file_regions4otherheatmaps.bed -b 4000 -a 4000 --missingDataAsZero -bs 50 

 plotHeatmap -m file_matrixcenter.gz -out HDFd2refcenter.png --dpi 300 --colorList '#FFFFFF,#FDF0E3,#FCE1C7,#FBD3AB,#FAC48F,#F8B573,#F7A757,#F6983B,#F58A20' --dpi 300 --whatToShow 'heatmap only' --refPointLabel 'Peak center'

With 'TSS':

the same code just changed

--referencePoint center

to

 --referencePoint TSS
sequencing chip-seq deeptools • 597 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by salamandra180

can you show the results? either the images or gunzip -c file_matrix*.gz | head

ADD REPLYlink written 9 months ago by Friederike2.3k

also, a peek into the peak files might be helpful

ADD REPLYlink modified 9 months ago • written 9 months ago by Friederike2.3k

i feel a bit silly, they're actually a bit different... but still don't understand why in the peak center heatmap the darker areas are not aligned among different regions. They should be right? https://imgur.com/a/5sPUa

ADD REPLYlink modified 9 months ago • written 9 months ago by salamandra180
1

they don't need to align perfectly, after all, this will depend on the structure of the peak and how the peak center was actually being determined.

you may wan to decrease the bin size (perhaps to 10bp), which will make the plot a little more smooth, but basically what these plots reveal is that there are some peaks with multiple local maxima

ADD REPLYlink written 9 months ago by Friederike2.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1181 users visited in the last hour