Hello,
I want to store detect my variants in a VCF format. For that I need to map my PE reads (100x2) to reference. What I have discovered however is that for a lot of my PE reads, the fragments size is smaller than 200bp, which means some PE reads overlap, increasing the coverage of a region artificially.
I thought I would merge the PE reads with SeqPrep to place all PE reads that overlap in a merged.fastq file.
My question is, how do I then map both unmerged PE reads and merged SE reads to the genome with bwa? I only know how to do it if it's only SE or only PE.
Also, does this approach sound reasonable?
Adrian
Biostar: http://www.biostars.org/p/97423/#97430
I want to store detect my variants in a VCF format. For that I need to map my PE reads (100x2) to reference. What I have discovered however is that for a lot of my PE reads, the fragments size is smaller than 200bp, which means some PE reads overlap, increasing the coverage of a region artificially.
I thought I would merge the PE reads with SeqPrep to place all PE reads that overlap in a merged.fastq file.
My question is, how do I then map both unmerged PE reads and merged SE reads to the genome with bwa? I only know how to do it if it's only SE or only PE.
Also, does this approach sound reasonable?
Adrian
Biostar: http://www.biostars.org/p/97423/#97430
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