User: Timze W

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Timze W40
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40
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New User
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Last seen:
1 week ago
Joined:
1 year, 7 months ago
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w******@gmail.com

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Posts by Timze W

<prev • 14 results • page 1 of 2 • next >
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Comment: C: will C-base re-synthesize during PCR in Bisulfite methylation sequence
... Yes, you are right. My picture just shows a un-methylation C site and its new chains after PCR. And my confusion is that many blogs say methylation C will keep C and un-methylation C will become a T, but during the PCR , it seems there will generate the un-methylation C. ...
written 16 days ago by Timze W40
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Comment: C: will C-base re-synthesize during PCR in Bisulfite methylation sequence
... Thanks. But sorry for my superficial understanding of methylation sequencing experiment, what puzzles me actually is how the PCR process prevents a new C synthesis, because there is still a G base in the other chains. ...
written 17 days ago by Timze W40
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will C-base re-synthesize during PCR in Bisulfite methylation sequence
... I knew that using bisulfite can turn unmethylated C to U, but I still have a problem about this technology: Supposed a non-methylated C in the forward chain now becomes U, but then during PCR, with a G in reverse chain, will it re-synthesize the C-base in the new chain (may be something happen jus ...
methylation bisulfite written 17 days ago by Timze W40
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Answer: A: Volcano plot: why is there big FC with big p-values?
... It seems you have the idea that bigger Fold-change expect to smaller p-value. But P-value and Fold-change are not necessarily related, fold change just reflects mean change, then P-value is not only depended by mean but also variance. (for example, if you perform the two sample students t-test ) ...
written 4 weeks ago by Timze W40
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Answer: A: Determine adapter sequence in RNA-seq samples
... The best solution is to ask your sequencing data provider. Typically, QC software (such as `fastQC`) can report some regular adapter types, while `trim-galore` can automatically detect and cut these adapters. ...
written 5 weeks ago by Timze W40
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Comment: C: Why DP and GT info in my VCF file are inconsistent?
... Thank you. And this is my puzzle, if the genotype is '0/0' , Why there are 23 reads for alt allele? ...
written 10 weeks ago by Timze W40
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Why DP and GT info in my VCF file are inconsistent?
... Here is part of my VCF file with two samples: > GT:AD:AF:DP:F1R2:F2R1:SB 0/1:73,4:0.061:77:27,1:46,3:31,42,2,2 0/0:333,23:0.065:356:160,8:166,15:155 I understand that GT stands for genotype, so, 0/1 means heterozygote and 73 reads support ref allele and 4 reads support alt allele ...
vcf gatk format written 10 weeks ago by Timze W40 • updated 8 weeks ago by Biostar ♦♦ 20
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What is the different if I call germline SNP/Indel with mutect and HaplotypeCaller?
... Hello, I have noted that, as designed for somatic variants caller, MuTect2 includes some logic to skip variant sites that are very clearly germline based on the evidence present in the Normal sample compared to the Tumor sample, for avoiding spending computational resources on germline events. An ...
gatk mutect haplotypecaller. written 3 months ago by Timze W40
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Comment: C: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
... As for hg38 data, you can download it through FTP annotation database directly. ...
written 6 months ago by Timze W40
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Comment: C: Are there any way to find DMR with the data in TCGA methylation level3?
... Thanks for your help. I have finally solved this problem, but what I use is the other tool called ChAMP., it can accept the beta value matrix as input. AND for the TCGAbiolinks, I have noticed it have this function, but when I read its code in GitHub, it seems do the same works for DMRs just as fo ...
written 12 months ago by Timze W40

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