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Non-unique alignment > 95% !!!
Hi guys,
After running some quality control on my bam files (removing (a) reads not passing chastity and (b) reads not aligned) I used Partek's FLOW to analyze the resulting files. What's showing up is that in my pre-QC files I have ~5% unaligned, ~5% aligned and ~90% unaligned whereas post-QC: ~0% unaligned, ~5% aligned and ~95% unaligned.
Is there another way to confirm that this indeed is the case? Any idea as to why this happened?
After running some quality control on my bam files (removing (a) reads not passing chastity and (b) reads not aligned) I used Partek's FLOW to analyze the resulting files. What's showing up is that in my pre-QC files I have ~5% unaligned, ~5% aligned and ~90% unaligned whereas post-QC: ~0% unaligned, ~5% aligned and ~95% unaligned.
Is there another way to confirm that this indeed is the case? Any idea as to why this happened?