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Old 09-10-2010, 03:52 AM   #1
Location: Dublin, Ireland

Join Date: Sep 2009
Posts: 22
Default MIRA output for Illumina mapping giving 100% coverage!

Hi all,

I've been using MIRA as I have both Illumina and 454 reads that I wanted to do mapping/assembly as well as semi-hybrid and hybrid assembly. However, when I use MIRA on the Illumina data alone for mapping with

"mira --project=0800 --job=mapping,genome,normal,solexa --fastq -SB:bft=gbf >&0800_Illumina_log_assembly.txt"

I get 1 contig of length 4,798,671 which is pretty much 100% coverage of the genome! I've used bwa and bowtie as well which give me a more realistic ~68-69% coverage. Can anyone tell me why/how MIRA is doing this? I've played around with the setting and read the documentation but I'm at a loss!


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Old 09-10-2010, 04:45 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

I'd ask on the MIRA mailing list, but Bastien also posts here.

My guess is different rules/settings for mismatch thresholds, but also MIRA isn't really doing a mapping but a guided assembly (it will extend the reference sequence(s) if it can).

Last edited by maubp; 09-10-2010 at 04:47 AM. Reason: typo
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