User: sudhirjadhao2009

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Posts by sudhirjadhao2009

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CexoR running error
... Dear All, Greetings for the day!! When I running CexoR, I am facing below error. Error in if (C != 0 && D != 0) { : missing value where TRUE/FALSE needed Calls: cexor Execution halted   Command used rep1 <- "CTCF_replicate1.sorted.bam" rep2 <- "CTCF_replicate2.sorted.bam" rep3 &l ...
cexor written 2.3 years ago by sudhirjadhao20090
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how to analyse chip-chip on normalized data without bpmap file or how to select bpmap file for your data(data downloaded from NCBI geo)
... Hello Everyone, I want to analyse chip-chip data. I have downloaded CEL file and normalized data file from NCBI geo. 1. To call peak using CEL file, I will need bpmap file. I have downloaded bpmap file from different sources.All have extension like M01R, M02R,  .. ,M14R. But for my data I will nee ...
starr chip-chip written 2.6 years ago by sudhirjadhao20090
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Comment: C: ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is d
... Thank you for replay. I got your point . but whatever number is common,  I want to extract id of those common peaks Below is the summary of my data.  summary(ol$peaklist)                                               Length Class   Mode si8444DHTR1S16                                 803   GRanges ...
written 2.7 years ago by sudhirjadhao20090
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ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
... I am finding overlapping region in two chipseq samples. The number of overlapping peaks in ven diagram are different from what you get in  ol1$overlappingPeaks and ol1$peaksInMergedPeaks. For specific peak the ven diagram number is same as in ol1$peaklist. But not for overlapping peaks. In example ...
chippeakanno written 2.7 years ago by sudhirjadhao20090 • updated 2.7 years ago by Ou, Jianhong1.2k

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