User: CY

gravatar for CY
CY30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 week, 5 days ago
Joined:
1 year, 11 months ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 40 results • page 1 of 4 • next >
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Answer: A: Immune repertoire sequencing community
... Hi Mikhali. Thanks for opening this discussion. I am new to Rep-Seq but interested in getting start to know all these. One question though after conducting some research: I saw lots of people using single cell sequencing (Smart-Seq) to sequencing T / B cell. I assume this is for evaluating the abu ...
written 6 weeks ago by CY30
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(Closed) Why adding adapter first and probe later, but not the opposite?
... I saw it is common to add adapter first and then use probe to grep interested fragments in lots of NGS protocol. I am wonder why don't we do the opposite? Would't that be more efficient since that way we can only target fragments being bind with probes and don't have to waste adapters on unwanted ...
ngs next-gen sequencing written 7 weeks ago by CY30
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Comment: C: Will random hexamer priming introduce SNP / SNV detection bias?
... You are right. A second thought of this bias: This will not cause bias in SNP / SNV calling right? Although it uneven reads coverage. The allele frequency will not be changed by this. ...
written 7 weeks ago by CY30
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Comment: C: Bwa And Bwa Mem Produce Different Alignments
... Perhaps this has something to do with the fact that bwa-mem uses local alignment and bwa-aln uses global alignment. The way you prepared you library may gets lots of reads cannot be completed aligned to the reference (meaning there are lots of mismatches in the middle). Reads like that are more acce ...
written 7 weeks ago by CY30
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Comment: C: Will random hexamer priming introduce SNP / SNV detection bias?
... A second thought of this bias: This will not cause bias in SNP / SNV calling right? Although it uneven reads coverage. The allele frequency will not be changed by this. Am I right? ...
written 8 weeks ago by CY30
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Will random hexamer priming introduce SNP / SNV detection bias?
... Certain hexamer primers are favored during PCR step and this will cause allele frequency bias in the alignment. I image this bias will affect SNP /SNV calling. Are there any tools correcting this kind of bias? Any comments are appreciated! ...
next-gen snv snp written 8 weeks ago by CY30 • updated 8 weeks ago by Pierre Lindenbaum98k
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Comment: C: Difference between Rad-Seq and amplicon seq
... Hi SNPsaurus Thanks for explaining. However, what do you mean "It is very difficult to choose a restriction enzyme or combination of enzymes that would sequence more than one SNP of interest" and "Having several thousand SNPs in a non-model organism allows many population analyses to be done"? It ...
written 8 weeks ago by CY30
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Comment: C: Difference between Rad-Seq and amplicon seq
... I read the paper and still felt little difference between capture based sequencing and Rad-Seq. Both are capturing region near which restriction enzyme which specific sequencing bind to. ...
written 8 weeks ago by CY30
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Comment: C: Difference between Rad-Seq and amplicon seq
... I can image it is cost-effective to selecting only the region near which the restriction enzymes bind and get high depth for population study. The questions is: Is the region selection (restriction enzyme selection) is entirely random? Or there are some sequence selection through the design of rest ...
written 8 weeks ago by CY30
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Comment: C: Difference between Rad-Seq and amplicon seq
... Then what is the purpose of this technique? If it is just random cutting, the purpose seems to be looking for any SNP or QTL within any regions. But you are not covering all the regions using this technique and you will probably missing lots of candidates. It seems not reasonable to me... ...
written 8 weeks ago by CY30

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