User: CY

gravatar for CY
CY130
Reputation:
130
Status:
Trusted
Location:
United States
Last seen:
15 hours ago
Joined:
2 years, 7 months ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 115 results • page 1 of 12 • next >
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Comment: C: SciClone not numeric error
... Hi Miller I am trying add CNV (called from VarScan) as input. The format is as following: 1 861322 2453157 -0.0003 The 4-th column is segment_mean. is this format right as input? The reason I am ask is because the output figure is a little weird. It does not show any peak around 50% VAF altho ...
written 15 hours ago by CY130
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Comment: C: why PCA for RNA-Seq but tSNE for scRNA-seq?
... Can I say PCA focus on the sample distance (variance) and can show outliers. On the other hand, tSNE focus on local structure at expense of long distance information and may mis-cluster some samples together when actually they are far away? ...
written 3 days ago by CY130
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why PCA for RNA-Seq but tSNE for scRNA-seq?
... I am under the impression that, in general, PCA is used for RNA-Seq but tSNE is used for scRNA-seq. Can anyone share some comments on why this is the case? is it because some intrinsic difference between mRNA and scRNA? ...
scrna-seq pca tsne rna-seq written 4 days ago by CY130 • updated 4 days ago by harold.smith.tarheel4.1k
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Comment: C: Inconsistency of allele depth in BAM and VCF
... I used Metect basically with default parameters. ...
written 18 days ago by CY130
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Inconsistency of allele depth in BAM and VCF
... We checked several alleles (locus) in both bam and vcf file. Almost all of them show a little bit high depth in bam file and a bit lower depth (AD) in vcf file. I guess this have something to do with variant caller filtering out some reads based on pre-defined criteria before make the variant callin ...
vcf allele depth variant bam written 18 days ago by CY130 • updated 18 days ago by Noushin N520
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Comment: C: Tumor Mutation Burden calculation: all_mut vs non_synonym
... The rest criteria are understandable. However, why non-coding mutations are not counted? What is the logic for this? ...
written 25 days ago by CY130
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CBS in CNV calling
... Can anyone kindly explain how CBS works for calling CNV? Seems like I could not find enough introduction anywhere. Really appreciate ...
cbs cnv written 25 days ago by CY130 • updated 25 days ago by Kevin Blighe19k
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RNA-Seq: Expression consistency across time point
... Now lots of expression analysis are done using RNA-Seq. Does anyone have any ideas how expression looks like between different time point? I guess the expression (same tissue from same individual) does not vary significantly, right? Otherwise it is pointless to do such analysis. Can anyone having th ...
expression rna-seq written 6 weeks ago by CY130
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Comment: C: Lack of consensus between NGS & Sanger sequencing on indels/mutations
... Yes, the first type is what I was talking about. It is a fixed probability depending on which reference you use. I am not sure about the second type you mention. In my expression, GATK also use the first type as prior. That is why --dbsnp arguments is used in HC / Mutect ...
written 6 weeks ago by CY130
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Comment: C: Lack of consensus between NGS & Sanger sequencing on indels/mutations
... I am a little confused about what you said in EDIT. The prior probability, P(Genotype), is defined in early study, such as 1KB or dbSNP, and the probability is fixed (sure the probability value depends on the read depth in that vcf file). When using sub-BAM instead of entire BAM, the read-depth ...
written 6 weeks ago by CY130

Latest awards to CY

Student 3 days ago, asked a question with at least 3 up-votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Centurion 9 weeks ago, created 100 posts.
Supporter 5 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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