[mira_talk] Question on mapping PacBio reads to reference
- From: "Foecking, Mark F." <FoeckingMF@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 3 Oct 2013 19:33:49 +0000
Hello. We have a set of scaffolds that were generated from PacBio reads for a
small genome, and we are trying to map these reads using the scaffolds as a
reference, so we can view the resulting .ace file as a pileup in EagleView and
look at frameshifts and SNPs and perhaps determine if they are real or not
(without PCR/sequencing). When we do this, some of the reads map to the
reference (perhaps 10-15% of them) but when we open the file in EagleView, we
find the reference sequence has changed - is MIRA making a new consensus and
showing that alignment? Is there a way of having the reads aligned to the
original scaffolds?
The files are a 1.1MB fasta reference file and a 633 MB fastq file of
filtered_subreads.fastq (a text file generated by the center that assembled the
scaffolds). The manifest file is:
project=GM262Gmapping
job=mapping, genome, accurate
parameters=-NW:mrnl=0
parameters=-OUT:ora=y
readgroup
is_reference
data=Mcap_assembly.fna
readgroup=reads
data=filtered_subreads.fastq
technology=text
I've also tried technology=pcbiohq with similar, though not identical results.
Any suggestions? Thanks for any information.
Mark F. Foecking
Research Specialist
Department of Veterinary Pathobiology
316A Connaway Hall
University of Missouri-Columbia, Columbia, MO 65211
(573) 882-1526 voice
(573) 884-5414 fax
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