Hi all,
I have made and assembled multiple Illumina libraries before (single and PE), however, the last couple of genomes had some very weird things going on that I have no explanation for. These are bacterial genomes and are approximately 6Mb. When I got the data back and looked at the reads only about half the genome was represented, and there seemed to be islands of high coverage (20x or higher) interspersed with regions with absolutely no coverage (like, 0). Again, this was pretty much random throughout the whole genome so that after final assembly I get thousands of contigs that are hundred(s) of bp long, but with gaps in between them of hundred(s) of bp. I sheared them with a sonicator, but this is not different than what I was using before. This is the first time I used homemade adaptors and primers though, but I got substantial amplification after PCR.
Any thoughts?
I have made and assembled multiple Illumina libraries before (single and PE), however, the last couple of genomes had some very weird things going on that I have no explanation for. These are bacterial genomes and are approximately 6Mb. When I got the data back and looked at the reads only about half the genome was represented, and there seemed to be islands of high coverage (20x or higher) interspersed with regions with absolutely no coverage (like, 0). Again, this was pretty much random throughout the whole genome so that after final assembly I get thousands of contigs that are hundred(s) of bp long, but with gaps in between them of hundred(s) of bp. I sheared them with a sonicator, but this is not different than what I was using before. This is the first time I used homemade adaptors and primers though, but I got substantial amplification after PCR.
Any thoughts?
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