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

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


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?

slumpy42 is offline   Reply With Quote