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SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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fail to call peaks on small chromosomes- sacCer3 #38

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Mac OSX
2) What error message was displayed?
Fails to call peak on smaller chromosomes for SacCer3 (chromosomes of size 230 
kb, 316 kb, and 270 kb- chr I, III, and VI)
3) What was the exact command you used that resulted in the error?
run.zinba(
  seq='data.bed',  
  input="none",
  filetype="bed",
  twoBit="sacCer3.2bit",
  winSize=200,
  offset=10,
  extension=200,
  basecountfile='data/basecount_file.basecount',
  align='align_athresh2_extension200/',
  selectmodel=T, 
  selectchr = "chrIX",
  selecttype = "dirty",
  selectcovs = c("gcPerc", "align_perc", "exp_cnvwin_log"), 
  interaction= T, 
  threshold=0.05,
  refinepeaks=0, 
  numProc=4,
  winGap=0,   
  FDR=FALSE,
  outfile="data_athresh2/outfile",
  printFullOut=1,
  method="mixture"
)

4) Please copy and paste any additional screen output that resulted from
running the command

Original issue reported on code.google.com by caitlinc...@gmail.com on 3 Dec 2012 at 5:49

GoogleCodeExporter commented 8 years ago 
Try reducing the window size to 20-50 base pairs, as this is a smaller genome

Original comment by homer...@gmail.com on 7 Dec 2012 at 1:44