Gowtham, Maybe slightly off topic but it finally comes into Artemis or ACT :-) We actually do not use abacas. We use several types of contig ordering/scafolding (depending on whether there is a reference and whether or not we have PE libraries). Mostly I layout contigs using BLAT to a reference (if we have one) and use the result to make a contig order/orientation list which is then joined by a perl script in correct order giving the option to insert recognisable/functional linkers between them. At that stage we also write out the FT file which can be loaded as a track. Example is below; The advantage of doing it like this was that we could extend these scripts with getting the coverage from the assembly files and pulling them as custom plots into Artemis as well. Alex
example FT: FT misc_feature 1..53 FT /label="Joiner" FT /colour=255 99 71 FT exon 54..22598 FT /label="700917_contig00117" FT /colour=152 251 152 FT misc_feature 22599..22651 FT /label="Joiner" FT /colour=255 99 71 FT exon 22652..23638 FT /label="700917_contig00089" FT /colour=152 251 152 FT misc_feature 23639..23691 FT /label="Joiner" FT /colour=255 99 71 FT exon 23692..29133 FT /label="RevCompl_700917_contig00127" FT /colour=135 206 250 FT misc_feature 29134..29186 =========== snip ========== ________________________________________ Van: Gowthaman Ramasamy [gowthaman.ramas...@seattlebiomed.org] Verzonden: donderdag 15 december 2011 15:50 Aan: Bossers, Alex; Julian Parkhill; Gowthaman Ramasamy CC: artemis-users@sanger.ac.uk Onderwerp: Re: [Artemis-users] Customizing crunch file in ACT... That's a wonderful idea. In fact I already load the contig's FT track (from Abacas's). But, it never occurred to me that we can modify it to load linker information as well. After Alex's email, I am started to wonder if the linkers are providing any value addition at all?. I will have to explore..... Thanks very much Alex. Gowtham PS: Are you using Abacas by any chance Alex? If so, can I ask couple questions offline. Thanks. On 12/14/11 11:26 PM, "Bossers, Alex" <alex.boss...@wur.nl> wrote: 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. ALex -----Oorspronkelijk bericht----- Van: artemis-users-boun...@sanger.ac.uk [mailto:artemis-users-boun...@sanger.ac.uk] Namens Julian Parkhill Verzonden: woensdag 14 december 2011 9:42 Aan: Gowthaman Ramasamy CC: artemis-users@sanger.ac.uk 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 ..." Julian. 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 > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users Julian Parkhill Tel: +44(0)1223 494902 _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
