User: ff.cc.cc

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ff.cc.cc1.2k
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HuGeF - Human Genetics Foundation

Posts by ff.cc.cc

<prev • 99 results • page 1 of 10 • next >
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Answer: A: Tools To Identify Compound Heterozygous Variants?
... ...just to enrich the survey/discussion...I recently faced the same task, and found also this paper: Filtering for Compound Heterozygous Sequence Variants in Non-Consanguineous Pedigrees Their tool is online here ...
written 3.8 years ago by ff.cc.cc1.2k
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Answer: A: Snp Annotation Tool
... Hi, I usually filter snps from exome data with Exomiser in conjunction with or as alternative to annovar. Sometimes also wannovar (a web interface to a annovar online server) revealed helpful ...
written 3.8 years ago by ff.cc.cc1.2k
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Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... I would suggest also bpipe that "...provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. ". It seems intriguing, anybody have experience with it ? Feature comparison: Tool | GUI | Command Line (*) | Audit Trail | ...
written 3.8 years ago by ff.cc.cc1.2k • updated 3.8 years ago by brentp22k
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Answer: A: Which Way Is Right? Roh Or Ibd
... I suggest you to first perform relatedness analysis, estimating the IBD coefficients and then plotting results into a dendrogram or MDS form. First check HW equilibrium and heterozygosity, then compute IBD with: i) with plink check the --genome command or ii) with R I suggest the SNPRelate packa ...
written 3.8 years ago by ff.cc.cc1.2k
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Answer: A: Change Notation Of Chromosome In Bam File
... Hi, I had the same task with my chomosome notation. This post helped me. About the crash, beware of samtools version. Someone experimented crashes before version 0.1.19 ...
written 3.9 years ago by ff.cc.cc1.2k
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Comment: C: Bam Header Edit
... I agree, the method worked fine for me, but I had to redirect the output of the samtools/reheader command to a newly created bam file, otherwise the file with the correct header is printed to the screen and then the remote terminal crashed: samtools reheader header_corrected.sam header.bad.bam &g ...
written 3.9 years ago by ff.cc.cc1.2k
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Answer: A: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
... Hi I suggest to combine R & Plink this way: > R code: > map2 = read.delim("file2.map", header=F, quote="") > map1 = read.delim("file1.map", header=F, quote="") > common.snps = which(map2$V2 %in% map1$V2) > write.table(map2$V2[common.snps], file="list.snps", sep="\t", col.names=F, ...
written 4.1 years ago by ff.cc.cc1.2k
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Answer: A: Kaplan-Meier Plot And Analysis As Online Resource
... Hi, if you like working with R/Shiny this link is quite interesting. With little changes I adapted the code to serve online analysis. Changing dataset is only a matter of file replacement ...
written 4.5 years ago by ff.cc.cc1.2k
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Answer: A: How To Generate Randomized Sequence Based On Sequence Already Known?
... R version: dna = unlist(strsplit("acctg", split="")) rand_dna = [sample(1:length(dna))] ...
written 4.6 years ago by ff.cc.cc1.2k
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Comment: C: Interpolate Genetic Map
... -start access -create an empty db -choose the 'external data' menu tab -choose text file -follow the wizard ...
written 4.6 years ago by ff.cc.cc1.2k

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