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Old 06-05-2014, 10:45 AM   #1
Junior Member
Location: Baja California

Join Date: Nov 2012
Posts: 1
Smile Student

Hello everyone,
I am running a mapping of a mithochondria 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 diferent genomes. I already check the reference file is the one I used for the mapping.

Thank in advance for any help!

Last edited by Dnate; 06-05-2014 at 01:46 PM.
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Old 06-05-2014, 01:00 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Duplicate post, already being answered on the MIRA mailing list:
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