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Old 10-12-2015, 07:31 AM   #1
slumpy42
Junior Member
 
Location: NYC USA

Join Date: Apr 2014
Posts: 3
Default In-dels Illumina vs. PacBio

Hello,

I have a PacBio-generated closed complete bacteria genome. I am aligning Illumina reads of the same strain to it using breseq, a pipeline which uses bowtie2 for read mapping.

The alignment finds 100s of insertions, all of them are in homo-polymer runs (AAA...) of nucleotides.

2 questions:

1) Is it known that Illumina produces extra nucleotides in repetitive regions, or that PacBio is too short? Or do they both have In-del problems?

2) How should I deal with this? Just ignore all of them?

Thanks,
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