[mira_talk] MIRA with error corrected PacBio
- From: "Vince S. Buffalo" <vsbuffalo@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 7 May 2013 20:56:03 -0700
Hi MIRA users,
I recently tested out MIRA with error corrected PacBio reads (via
PacBioToCA). After error correction our coverage was significantly lower
(2.7 according to MIRA; we had a high rate of read loss through the
PacBioToCA pipeline), but we ended up with a smaller number of contigs than
our Illumina-only de Bruijn graph assembly and a total number of bases very
close to our past assembly.
While initially happy with these results, we noticed that our read mapping
rate of Illumina reads to PacBio MIRA contigs (via bowtie2 with
--very-sensitive option) was remarkably lower (~48%) compared to our
Illumina reads mapped to Illumina-only contigs mapping rate (~97%). When we
map our Illumina reads to our error corrected PacBio reads, we see a much
higher mapping rate (around 84%), indicating that error correction isn't
adversely affecting the process.
I've looked and all contigs have reads mapping to them with decent
coverage, so it's not a subset of contigs with zero alignments causing the
low mapping rate. Our expected genome size is about 70Mb. Does anyone have
any insight into why our mapping rate is so low?
thanks,
Vince
--
Vince Buffalo
Statistical Programmer
Bioinformatics Core
UC Davis Genome Center
University of California, Davis
"There's real poetry in the real world. Science is the poetry of reality."
-Richard Dawkins
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