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Sorry, about the garbled message - here again:
Example output for "-b 1500" option
chr10 374751 375342 0.0
204404 73 NM_212479 chr10 170642 285200 + 170642 Closest
204404 73 NM_006624 chr10 170642 290576 + 170642 Closest
chr10 1300976 1301497 1.0
105529 594 NR_015376 chr10 1195707...
2009-09-30 00:17:39 UTC in USeq
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Just wanted to show an example:
Example output for "-b 1500" option
chr10 374751 375342 0.0
204404 73 NM_212479 chr10 170642 285200 + 170642 Closest
204404 73 NM_006624 chr10 170642 290576 + 170642 Closest
chr10 1300976 1301497 1.0
105529 594 NR_015376 chr10 1195707 1200611 + 1195707 Closest...
2009-09-30 00:16:22 UTC in USeq
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Hi,
I've been working with the FindNeighboringGenes tool and trying to limit the neighborhood with the -b option. However it seems that genes even far outside of this boundary are reported. Is that a bug in the software or am I using the -b option in a wrong way?
Example output for "-b 1500" option
chr10 374751 375342 0.0
204404 73 NM_212479 chr10 170642 285200 +...
2009-09-30 00:15:46 UTC in USeq
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Hi
I've been working with the FindNeighboringGenes tool and trying to limit the neighborhood with the -b option. However it seems that genes even far outside of this boundary are reported. Is that a bug in the software or am I using the -b option in a wrong way?
So, far I've filtered the FNG file with the following awk command:
awk 'FS="\t" { if($1 || ($4 && $4 <=...
2009-09-21 02:06:19 UTC in USeq
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Hi,
I've been trying to generate a spreadsheet of ERs using the EnrichedRegionMaker tool like you mentioned in the last paragraph based on only the chIP data. I'm getting an error message that the control is required.
The command I use is to retrieve the top100 regions:
java -jar useq-4.2/Apps/EnrichedRegionMaker -t ./PointData -f ScanSeqsResults/windowData52bp.swi -n 100
Error Message...
2009-07-29 05:23:50 UTC in USeq
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Hi, I'm having the same issue over here.
gcphrap 1.4 with phrap 1.080812 is giving compilation errors:
> make gcphrap
cc -O2 -c -o exp_file.o exp_file.c
exp_file.c: In function âwrite_exp_filesâ:
exp_file.c:1114: error: incompatible implicit declaration of function âour_allocâ
exp_file.c:910: error: previous implicit declaration of âour_allocâ was here
exp_file.c:1114...
2009-07-02 00:45:07 UTC in Staden Package
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Hi,
I was just trying to access the sources for useq but the CVS repository seems to be empty.
Is there a way to download them?
Thanks,
Deniz.
2009-07-01 00:17:41 UTC in USeq
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Hi,
I was looking at the recommended usage of useq which involves the ScanSeqs step - requiring a control sample.
Is there a way to assign confidence values to peaks purely based on statistical significance within the "treatment" PointData?
I was just wondering if I can use useq on an experiment designed without a control input sample.
Thanks,
Deniz.
2009-06-16 04:16:03 UTC in USeq
