Entering edit mode
9.9 years ago
Hello there
I have mapped whole genome sequences from Illumina Hiseq 2000 to the dog genome. We have mapped more than 15 genomes using BWA with default parameters. But we noticed a strange pattern in mapping of some genomes. These genomes had no reads mapped to some repetitive regions, the only common pattern that we saw was that all genomes were sequenced on the same flow cell. The other genomes sequenced on other flow cells had good coverage in the repetitive regions. Wondering what could be the cause for this ? Thank you for any explanation.
Just a quick question before I get lost in conjectures. Was the processing identical? That seems more like someone filtered low complexity reads for one given run.
Thank you SamuelL for the reply. Spoke to the lab and they said it was not filtered for low complexity reads.
No but the bioinfomatics people, did they do something ? Was is whole genome shotgun as well ? no capture or RNA-Seq ?
No the bioinformatics people also did not filter for low complexity reads. It was whole genome shotgun.
can you plot your coverage with respect to genic regions ? I suspect something weird is going on
Samuel I do not see any difference in the coverage of genic regions between the genomes. I did not know how to attach the coverage plot here
How long is the repeat region ?