MultiBigwigSummary of deepTools keeps on running for a long time

Question

[saha.shagnik]

I am trying to generate a merged bigwig file using multiBigwigSummary for using in the plotCorrelation tool in deepTools. However, the 8 files are running in this program for almost 5hours. How long does it usually take to generate the output file using this command in deeptools usually? I am extremely new to coding and computational biology. Need a little help on how to generate a fast efficient converged file for usage in plotCorrelation in the next step. The code which I used in Ubuntu terminal is as follows- $multiBigwigSummary bins -bs 100 -b input_CNT.bw input_ALP.bw H3K9ac_CNT.bw (8 such file names in all) -o mbs.npz

Answer 1

[Al Murphy]

Hard to say how long it should run especially since you don't give the spec of your machine but one thing that will increase runtime is -bs 100 which averages the genome in 100bp bins. The default of 10,000bps would run significantly faster

[Friederike]

one could also up the number of threads via the -p option to increase throughput