Question: How to speed up computeMatrix of deeptools?
0
gravatar for weiyanjia2008
4 months ago by
USA/Madison/UW-Madison
weiyanjia200830 wrote:

When I docomputeMatrix using all gene regions and extent to 0.5Mb of TSS for Replication timing signal analysis, it has been running for two days. Is there any setting that can speed up the running or other alternative tools to do this?

The code is as follow:

BIN=20000
WIN=500000
RBL=6000
R=hg38GencodeV32.bed 
computeMatrix reference-point \
 --referencePoint TSS \
 -S U2OS_RT_R2-X_z_score_normal.bedgraph.bw \
    Clone110_RT_R2-X_z_score_normal.bedgraph.bw \
    FUSClone110_RT_R2-X_z_score_normal.bedgraph.bw \
 -R $R \
 -a $WIN -b $WIN \
 --skipZeros \
 --missingDataAsZero \
 -p 30 \
 -out results/R2/matrix_RT_TSS_$R"_"$BIN"_WS_"$WIN.gz
software error • 143 views
ADD COMMENTlink written 4 months ago by weiyanjia200830
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