Thread: Erange
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Old 09-15-2009, 01:40 PM   #17
joshibros
Junior Member
 
Location: Storrs, CT

Join Date: Sep 2009
Posts: 1
Default ERANGE problem

Hello Everyone,

I am trying to run ERANGE 3.1 (http://woldlab.caltech.edu/rnaseq/) with my own ChIP-Seq dataset. I have eland_extended files for lane 1 & 2. I convert them serially to RDS using makerdsfromeland2.py script. Then I run ERANGE with the following command.

python ./findall.py EXP2vsEXP1 EXP2.rds ./output/EXP2vsEXP1.txt -control EXP1.rds -listPeak -revbackground -ratio 3 -nodirectionality

It runs for about 10 minutes and finally succeeds. The EXP2vsEXP1.txt file has the following information.

#enriched sample: EXP2.rds (7.8 M reads)
#control sample: EXP1.rds (7.1 M reads)
#enforceDirectionality=False listPeak=True nomulti=False cache=False
#spacing<50 minimum>4.0 ratio>3.0 minPeak=0.5 trimmed=10%
#minPlus=0.25 maxPlus=0.75 leftPlus=0.40 shift=0 pvalue=back
#regionID chrom start stop RPM fold multi% peakPos peakHeight pValue
EXP2vsEXP11 ref_chr9 83452778 83452862 7.3 3.1 57.3 83452819 7.0 2.5e-17
#stats: 7.3 RPM in 1 regions
#8 regions (37.6 RPM) found in background (FDR = 100.00 percent)


But i am pretty sure that there are more than one peak with this data set (from the peak files I received from the contractor company). Could someone help me where exactly am I doing wrong.

Regards,
PJ

Last edited by joshibros; 09-18-2009 at 07:49 AM. Reason: Naming Issues
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