Re: [Useq-users] Using USeq to call peaks without input

[David N. <Dav...@hc...>]

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