User: hxlei613

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hxlei61380
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80
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Location:
Bangladesh
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3 days, 5 hours ago
Joined:
3 years ago
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Posts by hxlei613

<prev • 43 results • page 1 of 5 • next >
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Question about PCA plot using RPKM/FPKM.
... Hi, after searching for how to draw PCA plot using FPKM, there is still a question confusing me. For example, I have a FPKM matrix (let's say *matrix_sample*) for sample1 sample2 .. sampleN control1, control2 ... controlN (column) and gene1, gene2 ... geneN(row). I want to check if the data have bat ...
fpkm pca rna-seq written 4 days ago by hxlei61380 • updated 4 days ago by Kevin Blighe30k
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how to detect association between SNP and expression?
... Hi, I want to find the association between SNP and expression in normal CD4+. However I only have 18 samples. If I have hundreds of samples I can do eQTL analysis. What can I do in this situation ? I haven't find any solution yet. Glad for any suggestion. Thanks. ...
expression association snp written 7 days ago by hxlei61380 • updated 7 days ago by Dhana70
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Are there needs to perform imputation for genotype generated from WGS ?
... I know imputation is usually performed for genotypes from chips. What if these genotypes are from WGS ? It's true that WGS is expensive for a huge population. WHat about your opinions ? ...
wgs imputation written 4 months ago by hxlei61380 • updated 4 months ago by YaGalbi1.3k
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How to infer allele specific expression gene without phasing information?
... Hi, I've read many papers about allele specific expression(ASE). Most of them have phasing data so it is reasonable for them to get allele specific expression genes. For those who don't have phasing information, they just perform test on heter-SNPs but they also get corresponding genes without detai ...
allele specific expression written 13 months ago by hxlei61380
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ensembl transcript id to gene symbol using biomart
... Hi. I am using biomart to convert ensembl transcript id to gene symbol. However there seems to be something wrong. Because in the output there is an ensembl transcript id which has two symbol. Here are my script. > ensembl <- useMart(host="dec2013.archive.ensembl.org", biomart = "ENSEMBL_ ...
R biomart ensembl written 14 months ago by hxlei61380 • updated 14 months ago by Emily_Ensembl16k
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Question about details of the calculation of bisulfite conversion rates.
... Hi! I wonder some details about the calculation of bisulfite conversion rates. 1. It seems that conversion rate can be calculated using all types of C ( CpG, CHH, CHG ) ? 2. How about the coverage of every single C? 5X or 10x ? Is there a threshold ? Another question about CpG methylation rates: ...
bisulfite conversion rates written 17 months ago by hxlei61380 • updated 17 months ago by Devon Ryan85k
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How to call mitochondrial SNP?
... Hello. I have searched this question on biostars already.But I am not satisfied with the result. MitoSeek need a control to call mutation.Well I dont have a control. I have seen many papers said they used GATK but they didnt clearify UnifiedGenotyper or HaplotypeCaller. I also see someone try to use ...
mitochondrial snp written 18 months ago by hxlei61380 • updated 18 months ago by devenvyas490
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(Closed) Heteroplasmy and homoplasmy in mtDNA
... I have read some papers inorder to get a better understanding about heteroplasmy and homoplasmy in mtDNA. But I am still confused about the definition of heteroplasmy and homoplasmy . Could someone please give an easily undertanding explaination ? Thank you very much! ...
mtdna heteroplasmy homoplasmy written 18 months ago by hxlei61380 • updated 18 months ago by jotan1.2k
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Comment: C: Bias plot from targeted bisulfite sequencing
... Hi,I wonder how to draw a mbias plot using bwameth ? I cant find the script on github.Thank you very much! ...
written 18 months ago by hxlei61380
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Comment: C: CpG coverage of BS-seq ?
... Hi, I updated my question to make sure I have expressed myself clearly. Thank you very much! ...
written 19 months ago by hxlei61380

Latest awards to hxlei613

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Question about RRBS mapping efficiency
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Questions about BreakDancer
Popular Question 3 months ago, created a question with more than 1,000 views. For Question about RRBS mapping efficiency
Popular Question 4 months ago, created a question with more than 1,000 views. For FastQC report about WGBS.
Popular Question 5 months ago, created a question with more than 1,000 views. For FastQC report about WGBS.
Popular Question 9 months ago, created a question with more than 1,000 views. For Question about RRBS mapping efficiency
Popular Question 11 months ago, created a question with more than 1,000 views. For Questions about BreakDancer
Student 18 months ago, asked a question with at least 3 up-votes. For Question about MEDIPS
Popular Question 20 months ago, created a question with more than 1,000 views. For Questions about DAVID
Supporter 2.1 years ago, voted at least 25 times.

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