User: SNPsaurus

gravatar for SNPsaurus
SNPsaurus40
Reputation:
40
Status:
New User
Location:
Eugene, OR
Website:
http://snpsaurus.com/
Twitter:
@SNPsaurus
Scholar ID:
Google Scholar Page
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 1 month ago
Email:
e***@snpsaurus.com

SNPsaurus provides nextRAD genotyping services.

Posts by SNPsaurus

<prev • 7 results • page 1 of 1 • next >
1
vote
0
answers
225
views
0
answers
Comment: C: Difference between Rad-Seq and amplicon seq
... A standard RADseq project sequences all regions adjacent to, say, the SbfI cut site. That may be 10,000 or more loci across a genome, but also could be just 0.1% of the genome. It is very difficult to choose a restriction enzyme or combination of enzymes that would sequence more than one SNP of inte ...
written 3 months ago by SNPsaurus40
0
votes
1
answer
678
views
1
answers
Answer: A: phylogenetic analysis: 2.5 millions SNPs in 33 samples?
... How about RAxML? http://sco.h-its.org/exelixis/software.html It has handled much larger populations on a small server, so may work for your needs. ...
written 2.2 years ago by SNPsaurus40
1
vote
1
answer
1.8k
views
1
answers
Answer: A: How does FreeBayes evaluates variants that did not meet the --min-alternate-coun
... The min-alternate-count flag is used to set a threshold for which an allele is evaluated in the population. So as long as --min-alternate-total samples meet the threshold then the allele is used at that site. It looks like you want to filter away individual genotype calls that don't meet the 5 depth ...
written 2.2 years ago by SNPsaurus40
0
votes
2
answers
1.0k
views
2
answers
Comment: C: ddRADseq and segregating SNPs
... Right, that's why I included the "If you sequence fragments that are 150-200 bp with 100 bp paired-end reads, you'll sample more of the genome and have more SNPs." I thought it might be helpful to start with the simpler case of always being 100 bp to show how it is done. Sequencing a size range is ...
written 2.2 years ago by SNPsaurus40
1
vote
2
answers
1.0k
views
2
answers
Answer: A: ddRADseq and segregating SNPs
... If you have 6500 digestion sites within your planned fragment size selection range, and sequence with 100 bp reads, then you will be sampling 6500 x 100 = 650 kb. Then if the SNPs are spaced every 1.5kb (30Mb/20000 SNPs), you should end up with ~400 SNPs total that you assay. If you sequence fragmen ...
written 2.2 years ago by SNPsaurus40
0
votes
1
answer
493
views
1
answers
Answer: A: demonstration or vision of the genotyping2sequencing development
... I've shown an image that builds off of images used to illustrate the tag SNPs assayed by fixed-content genotyping platforms. Imagine you are looking for the cause of a rare Mendelian disease. It could be a variant right next to a tag SNP and you would never see it on the chip, but would with sequenc ...
written 2.9 years ago by SNPsaurus40
1
vote
3
answers
2.1k
views
3
answers
Answer: A: Percentage Of Genome All Humans Share
... There probably isn't a single nucleotide shared by all humans. Each person has >10 random mutations, so in a population of 5 billion people there are >50 billion random mutations, or at least 10X coverage of the diploid genome. ...
written 4.1 years ago by SNPsaurus40

Latest awards to SNPsaurus

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 962 users visited in the last hour