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,
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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