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sunnyisgalaxy / moabs

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data
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Looking for /pillar_storage/pillar00/deqiangs/ref/mm9.chrom.sizes, I am using human #2

Open demis001 opened 7 years ago

demis001 commented 7 years ago

@sunnyisgalaxy

How to pass the chromosome size file to mcomp, I have seen hard coded search for mm9 chromosome size in the log

Initial command: mcomp -p 32 -c comp.UN.vs.TR.txt --doDmrScan=1 --doDmcScan=1 --dmrMethods=2 --minCredibleDif=0.1 --maxDistConsDmcs=300

Line from log:

running: egrep -v '^track|^browser|^#' dmc_M2_0_vs_1.bed > dmc_M2_0_vs_1.temp && bedToBigBed dmc_M2_0_vs_1.temp /pillar_storage/pillar00/deqiangs/ref/mm9.chrom.sizes dmc_M2_0_vs_1.bb && rm dmc_M2_0_vs_1.temp Couldn't open /pillar_storage/pillar00/deqiangs/ref/mm9.chrom.sizes

Thanks

Dangertrip commented 4 years ago

@demis001 Hi! This problem has been solved in our newer version. Please upgrade MOABS accordingly. Thank you for your interest in MOABS.