Hi A big thank you to Tim, Yealing and Alex for all the help!
Here is what I have done so far: I got help from a friend to write a perl script that transforms the coordinates in the blast result file to cumulative coordinates. This file can then be read as a feature in Artemis just fine and maps perfectly onto the contigs. I also made some progress with the alternative discussed with Tim, i.e., loading the contig file in Artemis and choosing "write all bases in FASTA format" and then blasting this file. I managed to avoid the memory related problems I had with blastall by using the blast+ package and the legacyscript included there. The blast results can then be read as a feature in Artemis without any problems. Of these two approaches I prefer the first one since this allows me to keep the original contigs. The "problem" I am having now is getting the names of the proteins into Artemis. The blast results only include the systematic name of the blast hits, not the full names in understandable English. I am sure I am just missing something very simple here, and will soon have a solution, but if anyone has a suggestion I would also be very interested in hearing about it. Still in the learning phase... Cheers, Henrik ________________________________________ Från: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk] för Yealing [yealingt+arte...@gmail.com] Skickat: den 29 april 2010 11:59 Till: Tim Carver Kopia: artemis-users@sanger.ac.uk; Henrik Lantz Ämne: Re: [Artemis-users] Multiple contigs and Blastall-results 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<mailto: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<mailto: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<mailto:Artemis-users@sanger.ac.uk> > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk<mailto: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
