4 ms·

I bought the Nebula 30x product and got my results quite quickly, in under three months. It's hard to tell if my experience is better than average or not, given

I bought the Nebula 30x product and got my results quite quickly, in under three months. It's hard to tell if my experience is better than average or not, given that people tend not to speak up about services when they're delivered on time. There may be some issues with the data quality. I happened to post about it a couple of hours ago: https://www.reddit.com/r/Nebulagenomics/comments/w8013t/rate_my_read_depth_and_reads/ https://www.reddit.com/r/Nebulagenomics/comments/w8013t/rate... My current best guess is that more data than usual were of bacterial origin, but I'll have to learn a bit more bioinformatics to test that.

mbreese 4y ago
It's hard to tell what the 12Mb of sequence they are calling "other" is. It could be bacterial, or a decoy contig that is used to capture low-quality reads. Sometimes you'll see reference sequences also include things like EBV. Or it could be the ALT assemblies that represent different ways of putting together the reference (like HLA differences). The fact that you got 39X raw reads is pretty good. Also, it is usually called hg38, not hs38... I'm not sure where that came from. If you want to be super accurate, you could also use GRCh38, but there are sometimes subtle differences between the two. https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19 https://gatk.broadinstitute.org/hc/en-us/articles/3600358909...
aroch 4y ago
Eh, your results look perfectly fine, especially for a budget sequencing run. Keep in mind there are a lot of repetitive DNA sequences that don't map well (search "mappability track" for more info). Depending on the reference they used, these may even be masked out and thus no alignment can even be attempted.