Hi everybody,
I ran a ZINBA analysis for FAIRE-seq study and found around 4,000 peaks... which seems to be very few as we should find around 100,000 according to this paper : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202292/
So I was wondering if somebody could has an idea why I found so few peaks?
(See below the options)
Thanks for your help!
run.zinba(
align='.../athresh1_ext134',
numProc=8,
seq=.../file.bed',
basecountfile='.../file.basecount',
filetype='bed',
outfile='.../output',
twoBit='.../GRCh37.2bit',
extension=134,
printFullOut=1,
refinepeaks=1,
input='none',
threshold=0.05,
FDR=T,
interaction=T,
selectchr='22',
selectcovs=c("gcPerc", "align_perc", "exp_cnvwin_log"),
selectmodel=T
)
I ran a ZINBA analysis for FAIRE-seq study and found around 4,000 peaks... which seems to be very few as we should find around 100,000 according to this paper : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202292/
So I was wondering if somebody could has an idea why I found so few peaks?
(See below the options)
Thanks for your help!
run.zinba(
align='.../athresh1_ext134',
numProc=8,
seq=.../file.bed',
basecountfile='.../file.basecount',
filetype='bed',
outfile='.../output',
twoBit='.../GRCh37.2bit',
extension=134,
printFullOut=1,
refinepeaks=1,
input='none',
threshold=0.05,
FDR=T,
interaction=T,
selectchr='22',
selectcovs=c("gcPerc", "align_perc", "exp_cnvwin_log"),
selectmodel=T
)
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