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Eye of the next-gen storm? pmiguel General 17 05-27-2010 04:58 AM

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Old 03-16-2012, 04:16 AM   #1
kalidaemon
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Location: Boston

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Default Storm help

Hi everyone
I've been running some transcription factor binding site analysis using the Storm and Motifclass utilities in the CREAD package. I got some interesting results using a functional depth cut-off and decided to run my data through again this time using a p-value cut-off as a sort of sanity check. As always with this sort of analysis, this opened a huge can of worms because there is very little agreement between results. I've got a couple questions about this that I was hoping some of you could answer:
1. I know that altering parameters in one's analysis can lead to different results. Should I be surprised/concerned that my results were so different?
2. Has anyone used Storm/Motifclass? What did you find were the best parameters for your particular data-set?
3. I've also played around with DME/Matcompare and Patser. Are there any PWM or non-PWM based transcription factor binding site analysis methods that you really like working with?
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Old 06-05-2012, 05:32 PM   #2
capricy
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where did you get a stand-alone copy of Patser? Could you please some sample command lines, and how did you format your input files? Thanks.
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