Question: illumina reads showing gaps in repetitive sequences
0
gravatar for vidhya.gnanasekaran
4.9 years ago by
European Union
vidhya.gnanasekaran0 wrote:

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. 

alignment illumina genome • 1.2k views
ADD COMMENTlink written 4.9 years ago by vidhya.gnanasekaran0

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. 

ADD REPLYlink written 4.9 years ago by Gabriel R.2.6k

Thank you SamuelL for the reply. Spoke to the lab and they said  it was not filtered for low complexity reads. 

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by vidhya.gnanasekaran0

No but the bioinfomatics people, did they do something ? Was is whole genome shotgun as well ? no capture or RNA-Seq ?

ADD REPLYlink written 4.9 years ago by Gabriel R.2.6k

No the bioinformatics people also did not filter for low complexity reads. It was whole genome shotgun.  

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by vidhya.gnanasekaran0

can you plot your coverage with respect to genic regions ? I suspect something weird is going on

ADD REPLYlink written 4.9 years ago by Gabriel R.2.6k

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 

ADD REPLYlink written 4.9 years ago by vidhya.gnanasekaran0

How long is the repeat region ?

ADD REPLYlink written 4.9 years ago by Gabriel R.2.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 645 users visited in the last hour