Alternatively (as we do it) we generate an EMBL FT track containing the layout 
of contigs (incl any rev complementing and/or linkers). Works quite well for us 
and keeps comparison files clean/original.

-----Oorspronkelijk bericht-----
[] Namens Julian Parkhill
Verzonden: woensdag 14 december 2011 9:42
Aan: Gowthaman Ramasamy
Onderwerp: Re: [Artemis-users] Customizing crunch file in ACT...

Gowthaman ,

The right hand scroll bar controls the display of links based on size of the 
hit (removing shorter hits up to 1kb). If you want to control the display based 
on the score, then right click in the centre window and select "Set Score 
Cutoffs ..."


On 13 Dec 2011, at 23:20, Gowthaman Ramasamy wrote:

> Hi Everyone,
> I trying to trick ACT to display linking bars from two different blast out 
> files.
> I have a chromosome at one side and newly scaffolded  chromosome on the other 
> side  (generated by ordering of contigs using Abacas). I want to display two 
> kinds of link between them.
> 1.  crunch file from Abacas. To show matching/ordered contigs. So there will 
> be only few super wide bars.
> 2.  tblastx outfile between these chromosomes (used MSPcrunch to match with 
> Abacas outfile output)
> I manually fuse both the files and use in ACT. It display links from both. 
> But, I want to make abacas crunch disappear most of the time.
> My naïve attempt was to change score in the Abacas crunch file to"zero" 
> artificially, so that I can block that link using the ACT 's middle window 
> scroll bar. But, it does not respond. I mean, it does not control the display 
> based on score.
> But, when I load un modified blastout file (with  -m 9) option, it seems to 
> control the display. Is it something a known issue.
> Better, yet, is there any better way to use two different crunch/blast out 
> files?
> Gowthaman
> PS: I can load one chromosome twice. But, anything else?
> _______________________________________________
> Artemis-users mailing list

Julian Parkhill
Tel: +44(0)1223 494902

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