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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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Compute matrix -a -b influence the signal #1062

Open Antony-1996 opened 3 years ago

Antony-1996 commented 3 years ago

When I use deepTools computeMatrix 3.1.2 to calculate the different TF binding signal around the peaks,I meet some problem. When we extend the -a -b region from 1kb,2.5kb,5kb,10kb,25kb to 50kb with the bin size also increase, the enrich pattern of different peaks changed.(python 2.7.15). Code: computeMatrix reference-point -S FOXA1.bigwig -R SE_enhancer.bed TE_enhancer.bed Open_region.bed -o Path_out/FOXA1.mat.gz --referencePoint center -b 1000 -a 1000 --binSize 10 -p 15 image (total 2kb region bin 10) image (total 5kb region bin 10) why these will happen,and we icontinue to increase the region length ,the signal for TE and OR continue to drop.

dpryan79 commented 3 years ago

Oh, that's incredibly strange. Can you post your bigWig files somewhere so we can debug this?

Antony-1996 commented 3 years ago

I downloaded bigwigs from Encode database. the Enocde ID for FXOA1 is ENCFF795BHZ.