User: Jimbou

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Jimbou690
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690
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Location:
Germany
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3 months ago
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5 years, 8 months ago
Email:
r************@gmail.com

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Posts by Jimbou

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Annotate genomic positions with dbSNP rsIds
... Thanks a lot. Started as you recommended, but switched to bcftools in the end. ...
written 4 months ago by Jimbou690
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Answer: A: Annotate genomic positions with dbSNP rsIds
... I will write down my solution as an answer for documentation purposes. I started as Pirerre recommended, but then I used bcftools instead of GATK. First, I created a header .txt file for the custom vcf file ##fileformat=VCFv4.0 ##fileDate=09052019 ##source=allchr_allvsall_sex_adjuste ...
written 4 months ago by Jimbou690
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Annotate genomic positions with dbSNP rsIds
... Although I already found some ways to annotate genomic positions with rsIDs using e.g. UCSC table browser, I'm not happy with that since I want a one-in-all linux script taking also strand issues (flipped alleles A-T vs- T-A or switched reference alleles) into account. What I have: chr posit ...
dbsnp position rsid chr tool written 4 months ago by Jimbou690
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Difference of CN probes and SNP probes on genotyping microchip arrays
... Is there a difference between copy number (CN) probes compared to SNP probes on SNP arrays such as the Affymetrix 6.0 SNP array? Physically there could be longer oligos for the CN probes? Do you have to analyse both probes differently, e.g. do tools such as PennCNV use both probes for CNV detectio ...
array affymetrix snp cnv written 2.2 years ago by Jimbou690 • updated 2.2 years ago by Biostar ♦♦ 20
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Comment: C: Loading IMPUTE2 output into R for eQTL analysis
... How you want to treat with the genotype certainity? ...
written 3.3 years ago by Jimbou690
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Comment: C: I cannot read data into R (read.affy)
... Your data doesn't fit into the `read.table` function. Perhaps it's your header making the problem. Change " " to "_" and try it again. You can also post a snippet of your data table and check the help page for the `?read.affy` function. ...
written 3.4 years ago by Jimbou690
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Comment: C: PLINK and 1000 Genome browser
... What have you tried so far? Did you checked this [comprehensivs list][1] of tools already? [1]: http://www.1000genomes.org/category/tools/ ...
written 3.4 years ago by Jimbou690
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Comment: C: CNV analysis for targeted genomic region
... I recommend [R][1] for this. Additional helpful packages are [cn.mops][2], [Gviz][3] or [Exomecopy][4] and some more. You can find a comprehensive list in this nice paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1 [1]: https://cran.r-project.org/ [2]: htt ...
written 3.5 years ago by Jimbou690
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Comment: C: CNV analysis for targeted genomic region
... You could try to calculate the coverage per gene/exon/target, median normalize over all/within sets, build a reference sample supposed to be copy number of two, calculate the ratio between target and reference sample and perform a cluster analysis for CNV detection per gene/exon/target. This is simi ...
written 3.5 years ago by Jimbou690
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Answer: A: Imputation for genotyping data
... As inferred in this [paper][1] > In principle, a phasing algorithm should be able to “learn” about desirable phasing configurations for a given study individual by pooling information across the reference panel and all other individuals in the study, and the phasing accuracy should increase wit ...
written 3.5 years ago by Jimbou690

Latest awards to Jimbou

Scholar 4 months ago, created an answer that has been accepted. For A: Gviz (Bioconductor/R) ordering of groups in AnnotationTrack
Epic Question 7 months ago, created a question with more than 10,000 views. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 12 months ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Great Question 16 months ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Aggregate multiple rows based on common values in given columns in R
Appreciated 21 months ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For TCGA Segement Mean, GISTIC and CNVs
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Great Question 2.1 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Supporter 2.2 years ago, voted at least 25 times.
Great Question 3.0 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Question 3.0 years ago, asked a question that was upvoted at least 5 times. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Popular Question 3.0 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Student 3.0 years ago, asked a question with at least 3 up-votes. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 3.3 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Popular Question 3.8 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Scholar 3.8 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Scholar 3.8 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Scholar 3.8 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 3.9 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Partial or complete overlap of two genomic ranges
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length

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