User: CY

gravatar for CY
CY90
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
12 hours ago
Joined:
2 years, 4 months ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 83 results • page 1 of 9 • next >
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Answer: A: Can I ignore somatic mutations that are also in dbSNP when analyzing cancer-rela
... Depending the one population frequency. Variants in dbSNP with high PF are highly unlikely to be driver mutation ...
written 1 day ago by CY90
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Comment: C: Reads aligning in unstranded RNA-Seq library
... I am aligning to genome, say using STAR. For a specific genomic location, if it is unstranded library, I may got both 'ACACAA' and 'TGTGTT'. The sequence of very location on reference genome is 'TCTGTT'. In this case, aligner still align both read to the reference, just different strand, right? Like ...
written 14 days ago by CY90
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Reads aligning in unstranded RNA-Seq library
... Unstranded kit does not distinguish reads strand in RNA-Seq library. If a particular read can be aligned to one transcript on one strand and to another transcript on another strand, How does aligner, such as STAR, handle this. Does aligner aligns the read to both transcript? Thanks ...
alignment rna-seq strand written 14 days ago by CY90 • updated 14 days ago by h.mon11k
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Comment: C: disadvantage of NextSeq 500 compared with MiSeq
... We went back and check the amount of DNA poured onto flowcell. The amount seems to be reasonable. Could this be caused by any other reason? Besides, why excessive amount of DNA on flowcell would cause this? ...
written 4 weeks ago by CY90
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what cause poly-G from NextSeq
... I have some samples sequenced on NextSeq and fastq data of some samples shown enriched poly-G reads. I did some research and found out these poly-G is caused by NextSeq's 2-colour chemistry not being able to distinguish "G" and "no signal". However, How does this problem occur? What is the possibl ...
nextseq written 4 weeks ago by CY90 • updated 29 days ago by chen1.5k
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Comment: C: ExAC includes WES of phenotyped population
... Thanks for sharing. However, I think, as singh opinion, it could be a control for Mendelian diseases, especially with high penetrance, right? ...
written 4 weeks ago by CY90
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ExAC includes WES of phenotyped population
... I have a question regarding ExAC. I am trying to retrieve SNP with corresponding allele frequency for my own research. However, I noticed that ExAC dataset includes a fair amount of WES of phenotyped population including diabetes, Schizophrenia & Bipolar and Myocardial condition. Wouldn't th ...
population exac snp written 4 weeks ago by CY90 • updated 4 weeks ago by Chris Miller19k
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Comment: C: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
... Yes, That would be best, The question is what we can do for the best if we only have, say RNA-Seq data. ...
written 5 weeks ago by CY90
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Comment: C: Infer somatic mutations without normal control
... Hi Merkus, really appreciate your comments. I got several questions though: For point 4, my goal is to removing heterozygous / homozygous germline mutation. Considering that tumor purity is hardly 100%, I consider allele frequency of 50% or near 100% to be germline. I am not sure why did you mentio ...
written 5 weeks ago by CY90
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Comment: C: Infer somatic mutations without normal control
... Agree. Thanks for sharing ...
written 5 weeks ago by CY90

Latest awards to CY

Supporter 10 weeks ago, voted at least 25 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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