Hello Nicole,
You're close, just provide to the EnrichedRegionMaker a score index and a score for the one sample scanned data. In this case use '-i 0 , -s 50' to use index zero (the sum of reads in the window) and 50 to select peaks that have 50 or more reads. I used to provide a poisson p-value based on a global lambda but it was so inaccurate as to be meaningless.
I wouldn't recommend this approach though. Best to download an input sequencing sample as close to the tissue/ organism you can. There are 100's of false positives that will come up in your data without a control.
Better yet use a second chIP sample under a different condition or a different time point as the control.
-cheers, D
--
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | dav...@hc... | Skype/iChat: LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2: http://bioserver.hci.utah.edu:8080/DAS2DB/genome
On 8/2/10 3:34 AM, "Nicole Cheung" <ms...@ca...> wrote:
Dear David,
I am writing to ask if I can USeq to call peaks on my ChIP-seq data
without input control? I followed the instructions and was able to run
ScanSeqs without an input control data, which gave me 3 folders called
"Sum", "Sum+" and "Sum-". However, I cannot work out a way to run
EnrichedRegionMaker as it requires a score and a corresponding index.
The examples use QValFDR, EmpFDR and Log2Ratio, but I don't think these
are available in my case (without an input). Could you please give me
some advices of what I can do to find enriched regions without using an
input control data?
Thank you very much in advance.
Best regards,
Nicole
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