User: Tafelplankje

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Tafelplankje120
Reputation:
120
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Location:
Netherlands
Last seen:
3 years, 3 months ago
Joined:
7 years, 4 months ago
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Posts by Tafelplankje

<prev • 15 results • page 1 of 2 • next >
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Pipeable command to Liftover (UCSC) builds?
... I was wondering if anyone has trick to make the UCSC LiftOver program pipable in bash ? (https://genome.ucsc.edu/cgi-bin/hgLiftOver)  As I understand the application creates files from files, which is quite annoying sometimes; it would be handy if it could use stdin and stdout for the input/output. ...
genome build liftover bash written 3.3 years ago by Tafelplankje120 • updated 3.3 years ago by RamRS20k
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Comment: C: converting vcf to haploview with keep phasing
... Please write in ENGLISH!! ...
written 3.6 years ago by Tafelplankje120
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Answer: A: GWAS on dosage data - interaction
... you could also use quicktest http://toby.freeshell.org/software/quicktest.shtml ...
written 4.1 years ago by Tafelplankje120
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Comment: C: GWAS on dosage data - interaction
... snptest does not handle SNP interactions. ...
written 4.2 years ago by Tafelplankje120
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Comment: C: GWAS on dosage data - interaction
... Large datasets and R are a pain in the ass... ...
written 4.2 years ago by Tafelplankje120
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Comment: C: GWAS on dosage data - interaction
... that version does not handle dosage data in combination with interaction... ...
written 4.2 years ago by Tafelplankje120
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calling 1000G SNPs/indels from ngs data (chipseq or other source)
... I would like to call known (e.g. from 1000G project) SNPs and indels from sequence reads, in my case a chip-seq project with 20 samples. Is there an easy way to call known SNPs/Indels ? (How) should i take into account the Indels/SNPs during allignment (because an indel is could be quite different f ...
indel alignment chip-seq snp sequencing written 4.3 years ago by Tafelplankje120
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Comment: C: Impute2 1000Genomes Imputation, Optimal Sliding Windows
... What is the best strategy for impute to reduce the samples after phasing and combining them again afterwards? ...
written 5.1 years ago by Tafelplankje120
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Impute2 1000Genomes Imputation, Optimal Sliding Windows
... I have a large data set which uses >20Gb/core when imputing 5MB regions, so i would like to use regions of 1MB or less if possible, at least, reduce as much as possible without loss of imputation accuracy. Impute2 uses the -int command to specify the region you want to impute, standard is ~5MB ...
gwas imputation 1000genomes written 5.1 years ago by Tafelplankje120
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Comment: C: What Are The Best Practices For Faire-Seq Analysis?
... The encode project refers to http://www.uwencode.org/proj/hotspot-ptih/ for most of the tracks (especially dnaseI sites) however most of the code is not available; i got it working up to hotspot calling but FDR calculations and peak calling are not publicly available. ...
written 6.2 years ago by Tafelplankje120

Latest awards to Tafelplankje

Appreciated 5.0 years ago, created a post with more than 5 votes. For How To Map Snps To Genes Based On Recombination Hotspots And Ld
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How To Map Snps To Genes Based On Recombination Hotspots And Ld
Student 5.0 years ago, asked a question with at least 3 up-votes. For How To Map Snps To Genes Based On Recombination Hotspots And Ld

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