Re: [Useq-users] 0 read peaks with ScanSeqs

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

Hello Noboru,

I'd try setting the peak shift to 0 and the window size to 200 for RNASeq
data.  I suspect something odd is occurring when the window size is
smaller than the peak shift. With RNASeq data it doesn't make sense to
shift the location of the read with a peak shift.  This is really only
applicable to chIP-Seq data.

-cheers, D 

On 5/24/12 12:14 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:

>     Hi David, I'm using ScanSeqs to find peaks in RNA-seq data using
>peaks shift = 100 and window size = 50 and I noticed that a considerable
>number of the peaks found are very short (<20 bp) and have 0 read.
>ScanSeqs reports BW_Sum  BW_Sum+ BW_SumT- such as 2.0 0 2.0, but when I
>overlap the peak with my reads, I find none.
>
>     Do you know what I could be doing wrong?
>
>
>java -Xmx7500M -jar mypath/USeq_7.6.9/Apps/ScanSeqs -t all_Point/ -s
>results -p 100 -w 50
>
>java -Xmx6000M -jar
>~/shared/programs/chip/USeq_7.6.9/Apps/EnrichedRegionMaker -f
>results/windowData50bp.swi -i 0 -s 0
>
>     I used -i 0 and -s 0 because I couldn't find information about the
>index number for BW_Sum and I actually wanted all the peaks so that I
>could filter myself later.
>
>     If you want to have a look at my .bed and .xls files, I put them at
>http://mnlab.uchicago.edu/download/
>
>
>     The last peak in the .xls file is only 19bp long and doesn't
>overlap any read.
>
>     I can postprocess the peaks, and filter by minimum number of reads,
>but I'm curious whether I'm doing something wrong.
>
>     Thanks!
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