Hi,
We have a bunch of assemblies where we have identified chimeric reads, some of which we have verified as genuine recombination and some of which we suspect are artifact from PCR jumping during library prep. Template DNA was un-amplified genomic DNA. One cause for concern is that the chimeras we suspect are artifact are tightly associated with regions of homology within our ref seq.
Can anyone point me to good examples of pcr jumping artifact in Illumina data so we can try and get an idea if there is any chance these reads may or may not be artifact?
We have run the same library prep and sequencing using pcr amplified template and do not appear to see the same patterns of chimeric reads but this may well be because there are so many chimeras from truncated amplicons coming though.
cheers,
The_Roads
We have a bunch of assemblies where we have identified chimeric reads, some of which we have verified as genuine recombination and some of which we suspect are artifact from PCR jumping during library prep. Template DNA was un-amplified genomic DNA. One cause for concern is that the chimeras we suspect are artifact are tightly associated with regions of homology within our ref seq.
Can anyone point me to good examples of pcr jumping artifact in Illumina data so we can try and get an idea if there is any chance these reads may or may not be artifact?
We have run the same library prep and sequencing using pcr amplified template and do not appear to see the same patterns of chimeric reads but this may well be because there are so many chimeras from truncated amplicons coming though.
cheers,
The_Roads