Hi I've had the same problem in the past. There sometimes are reasons why we do not wish to join the contigs before we send for a blast, for example once we join the contigs, the other contig informations are lost.
I've been able to map the blast results correctly in Artemis, but because I'm not a very good scripter, things might work or break using the bash-awk script that I have. So I usually end up doing it sort of manually for a lot of different people with different data sets. Here's how I do it: 1, we need a file containing <contig name> in the first column and <contig length> in the second column. The make or break problem is that in this file, the contig names must be arrange to the exact order as Artemis puts them. 2, from there, I use a script to generate a file with <contig name> in the first column and <cummulative contigs length at start of contig> in the second column. This can be done with excel too, if you're not familiar with scripting. 3, I then process the blastall result file, by modifying the start and stop coordinates (adding the cummulative contigs length at start of contig to the start and stop coordinate). After that, (usually if nothing bad happens) you will be able to just load the blastall result file in Artemis. Best thing is we get to keep all the details that we might or might not need. Cheers, -- yealing -- On Thu, Apr 29, 2010 at 5:02 PM, Tim Carver <t...@sanger.ac.uk> wrote: > Hi Henrik > > You have found the correct solution. It is just that the blast reports > coordinates from the start of the sequence and so they need joining up > before you do the blast. I am not sure why you get that memory error. If > you > have access to another machine you may want to try the blast there. > Alternatively you could possibly try a smaller number of contigs and then > use the EMBOSS application 'union' to join them back up. > > Regards > Tim > > > On 4/29/10 8:09 AM, "Henrik Lantz" <henrik.la...@mikrob.slu.se> wrote: > > > I was hoping I could get some help with a newbie Artemis question. Very > new to > > all this. > > > > I have made a denovo assembly of a fungus using MIRA and 454-data only. > The > > resulting fasta file with around 4000 contigs loads into Artemis fine. I > can > > check all the contigs, find ORFs etc. The problem appears when I want to > > import the results of a blastall search on the contig-datafile. All > > annotations from the blastall results are lumped into the first five > contigs, > > with the overwhelming majority in the first contig. Obviously not > correct. I > > am using the -m 8 flag for the blastall search. Looking through the > resultfile > > from blastall in a text editor I can see that the blastall search has > worked, > > and there are many interesting hits, but I would like to visualize the > results > > on the contigs. > > > > I read through the mail archive and found a user with a similar problem > > (http://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00463.html) > and > > it seems one solution might be to save the contigs as a long continuous > file > > in Artemis, and then use that in the Blastall search. But when I try that > I > > get an error message from blastall: > > > > blastall(33748) malloc: *** mmap(size=1048576) failed (error code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > Bus error > > > > I am running on MacOSX Snow Leopard with 20 GBs of memory. > > Any help to get an inexperienced user started would be very much > appreciated! > > /Henrik > > _______________________________________________ > > 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 >
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