User: vjain

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vjain0
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Posts by vjain

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Comment: C: MEDIPS - Annotation output explanation
... Thank you For reply ,  FOR QUESTION 2. How to get exact position of chromosome ? Please see columns chr | start | stop. Can you please elaborate this answer. because when i see the start and stop these showing some number with equal number of interval on the bases of window size (100). Actually ...
written 17 months ago by vjain0
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Answer: A: MEDIPS - Annotation output explanation
... Thank you For reply ...
written 17 months ago by vjain0
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MEDIPS - Annotation output explanation
... Hi ,  I run a full script of MEDIPS and got output like this --     chr start stop CF SampleC_result.bam.counts SampleD_result.bam.counts SampleC_result.bam.rpkm SampleD_result.bam.rpkm SampleC_result.bam.rms SampleD_result.bam.rms MSets1.counts.mean M ...
medips output written 17 months ago by vjain0
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Comment: C: MEDIP: Problem with MEDIPS.createSet
... Hi Lucas,  Solution to my previous error was just that I wrote : BSgenome = BSgenome.Sscrofa.UCSC.susScr3  instead of BSgenome = "BSgenome.Sscrofa.UCSC.susScr3"   Also, I am facing a new issue in MEDIPS.saturation, i.e. sr = MEDIPS.saturation(file = "/home/mobashirm/PRJ2017Nov2017/drmohan/ME ...
written 19 months ago by vjain0
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Comment: C: MEDIP: Problem with MEDIPS.createSet
... Hi Lucas I figured out the error, the next problem arising is the following: CS = MEDIPS.couplingVector(pattern = "CG", refObj = Set1[[1]]) Error in Set1[[1]] : this S4 class is not subsettable please help. Thank You ...
written 19 months ago by vjain0
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Comment: C: MEDIP: Problem with MEDIPS.createSet
... Hi Lukas I tried giving the path and got the following error: Error in as.environment(pos) : no item called "paste("package:", BSgenome, sep = "")" on the search list In addition: Warning message: In ls(paste("package:", BSgenome, sep = "")) : ‘paste("package:", BSgenome, sep = "")’ converte ...
written 19 months ago by vjain0
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MEDIP: Problem with MEDIPS.createSet
... hESCs_MeDIP = MEDIPS.createSet(file = reads1, BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq, window_size = ws) Error in strsplit(file, "/") : non-character argument I uploaded my bam file named "reads1" using readGAlignments in R. Later I come across this error. I even edited ...
bsgenome medips medip-seq written 19 months ago by vjain0 • updated 19 months ago by Lukas Chavez510

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