When I do
computeMatrix 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