Re: [Useq-users] peak out of chr range

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

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.
> 
> 
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