[mira_talk] Alignment problem
- From: Dante Magdaleno <dante.soy@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 5 Jun 2014 10:28:49 -0700
Hello everyone,
I am running a mapping of a mitochondria from a microalgae with 100 bp
pair-end illumina reads from HiSeq 2500. I am using mira 4.0.2 on Bio-linux.
After the mapping is done, I use miraconvert to convert the file.maf to
file.sam, then with samtools I convert file.sam to file.bam, sort and index
the file to make the mpileup and call SNP's. My problem is that the length
of the alignment (28647 pb) obtained from MIRA is larger than the reference
sequence (28331)that I used for mapping, so when I call SNP's it is like I
am doing an alignment with two different genomes. I already check the
reference file is the one I used for the mapping.
Here the manifest parameters
project = mito
job=genome,mapping,accurate
parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no
readgroup
is_reference
data = salina_mito.fa
strain = D-salina
readgroup = Data Illuminapairedlib
autopairing
data = S_GCCAAT_L002_R1_002.fastq S_GCCAAT_L002_R2_002.fastq
technology = solexa
strain = D-salina
Thank in advance for any help!
Dante
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