Re: [Useq-users] EnrichedRegionMaker Error

[David N. <dav...@gm...>]

Yes, that explains it.  The MRSS only provides two scores per window
unlike ScanSeqs so you need to adjust what the indexes are.  In this case
use '-I 0,1 -s 20,1' to threshold 20 (0.01) for the FDR and 1 for the
log2Ratio.

With one replica though you will get a very conservative estimation of FDR
from DESeq (this is what MRSS uses), thus I'd suggest reducing the
stringency to 10 or 8.

-cheers, D

On 10/26/11 9:32 AM, "Baker, Richard" <Ric...@um...> wrote:

>*********** 10/26/2011 11:07:34 AM ***********
>java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f
>/Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -t
>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointData
>/Rep0 -c 
>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData/R
>ep0 
>
>
>Launching...
>Looking up indexes...
>
>Please enter one or more of the score indexes from below:
>	0	FDR
>	1	Log2((sumT+1)/(sumC+1))
>
>It looks as if the xxx.swi file contains only FDR and log2() information
>and I gave ERM three criteria to check.  Running with -i 1 -s 2 worked
>fine.  Thanks for the help.
>
>I only recently discovered USeq.  I've been using MACS and PeakSeq for
>peak calling (they give essentially the same results), and I probably
>won't change now that we're 90% finished with our analyses.  However,
>I've already found many of USeq's other programs extremely useful and
>easy to use (I've been using the GUI Wrapper on my iMac with 8G RAM).
>Thanks for making them available!
>
>*************************************************
>Richard Baker, PhD
>Department of Microbiology and Physiological Systems
>UMass Medical School
>55 Lake Avenue N.
>Worcester, MA  01655
>508-856-6046
>
>On Oct 26, 2011, at 10:40 AM, David Nix wrote:
>
>> Hello Richard, 
>> 
>> Would you mind running the app without the -s and -I options and have it
>> print out the indexes for this swi file?
>> 
>> "java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f
>> /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip"
>> 
>> -cheers, D
>> 
>> On 10/25/11 1:45 PM, "Baker, Richard" <Ric...@um...>
>>wrote:
>> 
>>> EnrichedRegionMaker consistently throws the following error when I try
>>>to
>>> process an xxx.swi file produced by MultipleReplicaScanSeqs:
>>> 
>>> *********** 10/25/2011 03:30:37 PM ***********
>>> java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f
>>> /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -s 20,20,1 -i
>>> 1,2,4 -t 
>>> 
>>>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointDa
>>>ta
>>> /Rep0 -c 
>>> 
>>>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData
>>>/R
>>> ep0 
>>> 
>>> 
>>> Launching...
>>> 25	Sub Window Size
>>> 
>>> Processing binaryWindowData.swi.zip...
>>> 	400	Max gap 
>>> 
>>> Error: max score index is greater than the number of scores!
>>> 
>>> ERM runs fine if called through ChIPSeq using the raw alignment files.
>>> What's up?
>>> 
>>> 
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>> 
>> 
>
>