Nobody know the answer of my problem? Is it too confusing? After run 454 reads by using MIRA and BAMBUS, I extract the longest scaffold and treat it as a backbone. I hope that I able to polish this longest scaffold by using Illumina reads to get better assembly result. I just confusing how to use MIRA to polish my longest scaffold and get better assembly result. Thanks again for everybody. best regards edge On Fri, Oct 16, 2009 at 9:45 AM, Chia Jing Yi <cjyxiaodi1@xxxxxxxxx> wrote: > Thanks a lot, Bastien. > I feel a bit confusing at the part of "Mapping assemblies" and "De-novo > hybrid assemblies" > For example, I got a bacteria genome which sequencing by 454 technique and > Illumina technique separately. > > For 454 technique read (included standard and paired-end sff file), > I follow the "Instructions of scaffolding MIRA 454 contigs & 25KB > paired-end data with BAMBUS" paper to create scaffold fasta file. > I extract the longest 454 scaffold fasta out. Got a file named as > "454_reads,fasta" now. > > For Illumina technique read, > Initially I got two files named as Illumina.fasta Illumina.fasta.qual > I follow the "De-novo Solexa only assemblies" without paired-end. > It worked perfectly by MIRA. > > Confusing part: > For getting best bacteria genome assembly back by combination of 454 > technique and Illumina technique reads. > At De-novo hybrid assemblies, All reads de-novo: > I just throw all > 1. Paired_end_in.454.fasta Paired_end_in.454.fasta.qual > Paired_end_traceinfo_in.454.xml > 2. Standard_end_in.454.fasta Standard_end_in.454.fasta.qual > Standard_end_traceinfo_in.454.xml > 3. Read_in.solexa.fasta Read_in.solexa.fasta.qual > And running the command: > > mira --project=bchocse --job=denovo,genome,normal,454,solexa > >&log_assembly.txt > > or > > At De-novo hybrid assemblies, Long read first, then Solexa: > 1. No idea how to deal with it because I not sure what is the > hybrid_backbone_in.caf refer to? > > Hope anybody can help me solve this problem. > My main purpose is using the reads from 454 technique and Illumina > technique read to get "good" assemblies. > > best regards > edge > > > On Fri, Oct 16, 2009 at 8:20 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote: > >> On Freitag 16 Oktober 2009 Chia Jing Yi wrote: >> > Refer to "Solexa sequence assembly with MIRA3", at the part of De-novo >> > hybrid assemblies ( Solexa + ...). >> > Can I know what is the format of input file should look like? >> >> Currently the default format for 454 is FASTA and for Solexa also. The >> latter >> may change to FASTQ in 3.0.0. >> >> Regards, >> Bastien >> >> >> -- >> You have received this mail because you are subscribed to the mira_talk >> mailing list. For information on how to subscribe or unsubscribe, please >> visit http://www.chevreux.org/mira_mailinglists.html >> > >