To re-order your scaffolds based on synteny, try running ABACAS which is available from:
http://www.sanger.ac.uk/resources/software/pagit/ -Matt Berriman On 05/01/2012 11:01 am, "Tim Carver" <[email protected]> wrote: > Hi Astrid > > When you do the blast between the assembled sequence and reference sequence > both sequences need to be in single fasta format (i.e. not multiple fasta). > The assembled sequence is likely to be in a multiple fasta format, so you > will need to load that into Artemis first and save it out as a single fasta > (from the menu: File->Write->All Bases->FASTA format). Then repeat the blast > comparison using this and the coordinates for the blast hits will appear > correctly in ACT along all scaffolds. > > I am not sure why your scaffolds are ordered by size and how likely that is > for your assembled sequence. > > Regards > Tim > > On 1/5/12 9:36 AM, "Astrid von Mentzer" <[email protected]> wrote: > >> Hi, >> >> I have an assembled sequence (Velvet) which I have compared to a reference >> sequence in ACT. I have run a blastall between the sequences. When I view the >> comparison in ACT, the scaffolds are ordered in size with the biggest first >> and only the biggest scaffold is compared to the reference sequence. >> >> What I wonder first is: Why are the scaffolds ordered according to size? How >> do I make a comparison between all scaffolds (the whole sequence) to the >> reference strain and not just one scaffold? >> >> I am new to this so please describe in detail so I understand. >> >> Cheers, >> Astrid >> >> >> _______________________________________________ >> Artemis-users mailing list >> [email protected] >> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
