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From: Sanjit S. B. <san...@gm...> - 2015-04-21 22:39:31
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Hey! I have a 30Mb scaffold that was assembled using optical maps. I would like to align it to a 3Gb long reference assembly. Given the method through which this scaffold was constructed, it should align to a region in the reference, roughly the same size as itself. I am currently running nucmer with the -c 100 flag, and I get a very large number of fragmented alignments, the longest of which is under 1Mb. Is there any way I can alter the flags to get a larger, less fragmented alignment, for this particular case? Any suggestions are appreciated. Thanks! On Tue, Apr 21, 2015 at 10:25 AM, Adam Phillippy <aph...@gm...> wrote: > Hi Sanjit, > There is no easy way to switch the reference and query once the alignment > is computed. > > What do you intend to use show-tiling for? The 'delta-filter' program can > be more flexible and useful for some tasks. If you run 'delta-filter -r' it > will select the best alignments for each of your smaller reference > sequences mapped to the larger query. If you run 'delta-filter -q' it will > select the best alignment covering each region of your large query, which > will (in effect) be similar to a tiling path of the best reference > alignments across the query. > > Hope this helps, > -Adam > > > On Tue, Apr 14, 2015 at 9:45 PM, Sanjit Singh Batra < > san...@gm...> wrote: > >> Hey! >> >> As mentioned in the manual, I switched the reference and the query while >> using nucmer, since the reference was very large, and much larger than the >> query. Now, I would like to run the show-tiling module on the resulting >> delta file(This feature was the primary reason I started using mummer). >> However, since the reference and query are switched, it tiles the reference >> chromosomes over contigs, which is not what is desired. >> >> So, is there a script that can switch the reference and the query in a >> delta file? >> >> Any suggestions are greatly appreciated. Thanks for your time! >> >> >> ------------------------------------------------------------------------------ >> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >> Develop your own process in accordance with the BPMN 2 standard >> Learn Process modeling best practices with Bonita BPM through live >> exercises >> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- >> event?utm_ >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >> _______________________________________________ >> MUMmer-help mailing list >> MUM...@li... >> https://lists.sourceforge.net/lists/listinfo/mummer-help >> >> > |