Odd that a peak could have been called at the terminus?
What's happening is that 1/2 the read length is added onto each end of the
EnrichedRegion. This could push the boundary off into the never never.
What I don't understand is how an alignment was made at the telomere where
repetitive sequences dominate. Are you filtering for unique alignments? I
wouldn't use any repeats in the analysis. Lots of aligners such as Bowtie
will by default pick a random repeat to assign a repeat read. I'd recommend
excluding these from typical chIP-seq analysis unless you're doing something
unusual with heterochromatin.
-cheers, D
On 1/12/11 4:43 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:
> Hi David, occasionally, Useq reports a peak ending outside a chr.
> Is anybody else in this mailing list seeing this?
>
> I verified my input .bed file and the highest end coordinate for
> chr19 is 61,342,406 (chr19 ends at 61,342,430), but Useq generated a
> peak from 61,338,222 - 61,342,436.
> Not a big deal, but maybe it's something easy to fix for the next
> release.
>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users
|
