Comments (3)
I am running on chr10_intrachr Hi-C data of rao.(GM12878) by " -m 3" usage
there are 128M cis PETs in this chr
and I find that over 50Gb memory is used and cloops keeps running after 1 day.
So, what is the expect running time according to your past test
Dear user,
Please increase the -minPts. -m 3 (-m 3 equals -eps 5000,7500,10000 -minPts 20,30,40,50) was set for total 200M cis-PETs, please try -eps 5000,10000 -minPts 50,100 or larger for first trial for your data. Larger minPts, the memory could be decreased. More eps more loops will be detected. The speed indeed depends on the computer and settings. Previouse our largest chr1 may use 30G memory and finish clustering within about 5 hours.
Lookforward to your good results.
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Thanks for your reply
I came on other test in usage "-eps 5000,10000 -minPts 50,100 -hic" and various data depth on chr10
18M cis PETs cost 4.5h, 10M cost 2h , 6M cost 1h, estimate as O(num of reads)
Another question is that. what is the accurate loop output?
by -j I got two output file : ‘xxx.loop' & 'xxx_loops_juicebox.txt' that have thousands and dozens lines respectively. Which to treat as number of loops? or to use FDR threshold on 'xxx.loops' to get true loop position?
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Related Issues (20)
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