User: Floris Brenk

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Floris Brenk770
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3 years, 5 months ago
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Posts by Floris Brenk

<prev • 156 results • page 1 of 16 • next >
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Comment: C: Chromosome Y imputation, any good reference panels?
... Ok thanks for your reply! As a follow up, are you aware of any tools that can identify the haplotype group based on plink data? ...
written 16 days ago by Floris Brenk770
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Chromosome Y imputation, any good reference panels?
... Hi all, Is anyone aware of a good reference panel for chromosome Y imputation? I know you could use 1000G, but I am more looking for a larger and more recent reference panel. Like the https://imputationserver.sph.umich.edu/ size.. ...
imputation chry genotyping written 17 days ago by Floris Brenk770
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... Ok thanks for your reply! Looks like it is working. BTW Do you have any ideas about chromosome Y imputation? ...
written 18 days ago by Floris Brenk770
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Comment: C: Cannot remove subjects from Plink files
... The only explanation I can think of is that maybe the file format e.g. the spacing is different in the keep file or that plink cannot find the file... Try to extract a few lines from your map file and make a new includesubjects.txt with some random samples based on that and try it again. ...
written 4 weeks ago by Floris Brenk770
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... No not yet, but they just emailed me saying that next week they will come up with a guide/pipeline how to deal with chromosome X ...
written 4 weeks ago by Floris Brenk770
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Imputation of chromosome X using the Michigan imputation server
... Hi all, Im trying to impute some genotype data on the Michigan imputation server (https://imputationserver.sph.umich.edu/ ). For autosomes this works perfect and straightforward. However for chromosome X I ran into some trouble. Initially that Eagle v2.3 does not work on chromosome X and so you nee ...
imputation genotypes chrx written 5 weeks ago by Floris Brenk770 • updated 19 days ago by chariko20
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Answer: C: finding unique mutations from a multi-sample VCF
... Why not filter on minor allele frequency using vcftools? Using for example --max-maf you can set the maximum in this case you have 8 alleles so max allele frequency would be 0.125 http://vcftools.sourceforge.net/man_latest.html ...
written 5 weeks ago by Floris Brenk770
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Creating basic phylogenetic trees of human haplotype in R
... Hi all, I'm trying to create some basic phylogenetic trees of human haplotype and looking for some feedback. I started using the R package "phangorn" (https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.pdf) and it all looks pretty striaghtforward when having the proper .dna format. I ...
phylogenetic R haplotype written 5 weeks ago by Floris Brenk770
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Comment: C: How to annotate TTS or TES
... If you got human or mouse data, you could download the FANTOM5 (http://fantom.gsc.riken.jp/data/) annotated promoters and use an intersecting tool to annotate your start sites with that. ...
written 3 months ago by Floris Brenk770
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tool for identifying structural variation for DNA
... Hi all, I have a large stretch of DNA (about 75 kb) and I suspect there is some structural variation in there like duplications and maybe inversions. Also maybe this variation is already a bit "old" (meaning happened a long time ago thru evolution) so e.g. duplications are likely not to be 100% iden ...
cnv dna written 3 months ago by Floris Brenk770

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Scholar 3 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 6 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
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Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 9 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 10 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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Scholar 12 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
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Popular Question 19 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
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