User: kynnjo

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kynnjo40
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40
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New User
Location:
United States
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3 weeks, 5 days ago
Joined:
6 years ago
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k*****@gmail.com

Posts by kynnjo

<prev • 23 results • page 1 of 3 • next >
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On the conventions for annotating the position of insertion and deletion variants
... **Preamble** *(Skip this section if you're in a hurry!)* This query is about the rules/conventions for annotating the positions of indel variants in genotyping data. The query is phrased in terms of the field (or column) names used by Illumina in the manifest files it provides for its genotyping ...
genome indels variant genomics genotyping written 27 days ago by kynnjo40
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Answer: A: How to extract ~2M short sequences based on coordinates from a 3G fasta file?
... Shortly after I posted this question I found that samtools faidx -r ... does what I need. ...
written 4 weeks ago by kynnjo40
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How to extract ~2M short sequences based on coordinates from a 3G fasta file?
... (Sorry for the Bioinformatics 101 question!) I have a file with ~2 million sets of coordinates (chromosomebegin-positionend-position), corresponding to short (~50nt) human genomic sequences (hg19). I want to extract the actual sequences from a human genome assembly 19 fasta file (~3.0G). I imagin ...
genome assembly sequence written 4 weeks ago by kynnjo40
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Comment: C: How to use plink to consolidate multiple single-sample vcf files?
... Thank you. Just from your answer I can guess one reason for my failure to find what I was looking for: I thought this would be a single command operation. In my original post I neglected to mention that I am using plink version 1.90b, for backward-compatibility with the rest of the project I am wo ...
written 4 months ago by kynnjo40
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How to use plink to consolidate multiple single-sample vcf files?
... I have a few hundred single-sample vcf files that I need to consolidate into a single vcf file. My understanding is that plink is one of the many tools that one can use for doing this. I would prefer to use plink if possible, even if it is not the best one, because I am already using plink for oth ...
vcf plink snp genotyping written 4 months ago by kynnjo40
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How does plink compute n_geno ("number of potentially valid call(s)")?
... I want to compute a call rate from the output I get by running plink with the `--missing` flag. The plink-generated output does not provide a call rate as such, but I am hoping to be able to derive such a call rate from the information it does put out. For the purpose of calculating call rates, th ...
plink genotyping written 13 months ago by kynnjo40 • updated 13 months ago by chrchang5237.1k
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Unix command-line alternatives to GenomeStudio's clustering?
... Up to now, our group has done (re-)clustering of genotyping data using a Windows-based interactive graphical tool, GenomeStudio, provided by Illumina. I am looking for an alternative that I can do from the Unix command-line. Does anyone know of one? ...
clustering genotyping written 19 months ago by kynnjo40
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On conventions for human chromosome numbering in file names (1 vs 01, etc.)
... I am relatively new to bioinformatics, though I have been doing scientific programming for a few years now. The following example is illustrative of a recurring situation: % ls -1 chr10.txt chr11.txt chr12.txt chr13.txt chr14.txt chr15.txt chr16.txt chr17.txt ...
bioinformatics genomics written 20 months ago by kynnjo40 • updated 20 months ago by Pierre Lindenbaum129k
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Where does Illumina make MEGA_Consortium_v2_15070954_A2.csv available?
... I am trying to replicate some methods from a paper, where the authors refer to the file MEGA_Consortium_v2_15070954_A2.csv ...provided by Illumina, but my Google searches have not revealed the URL where Illumina makes this file available. Does anyone know? (**NB:** Since I need to document m ...
illumina genotyping written 21 months ago by kynnjo40
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How to make small subset of large genotyping dataset with plink?
... I have a collection of genotyping files, that, for the purpose of this question, I will call big.bed, big.ped, big.fam, big.map, big.vcf, etc. This dataset has information on ~1.8M SNPs and 877 samples. I also have a list of ~1000 SNPs in a file wanted_snps.txt, one SNP per line. I want to genera ...
snp written 21 months ago by kynnjo40 • updated 21 months ago by Inquisitive8995170

Latest awards to kynnjo

Scholar 4 weeks ago, created an answer that has been accepted. For A: Accessing UCSC mysql DB: ERROR 1045 (28000): Access denied for user 'genome'
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to extract ~2M short sequences based on coordinates from a 3G fasta file?
Popular Question 4 months ago, created a question with more than 1,000 views. For Looking for clean list of gene names for UCSC's HG19
Supporter 19 months ago, voted at least 25 times.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Looking for clean list of gene names for UCSC's HG19
Great Question 4.1 years ago, created a question with more than 5,000 views. For R package for GSEA
Popular Question 4.1 years ago, created a question with more than 1,000 views. For R package for GSEA
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Accessing UCSC mysql DB: ERROR 1045 (28000): Access denied for user 'genome'
Popular Question 4.2 years ago, created a question with more than 1,000 views. For R package for GSEA
Scholar 4.7 years ago, created an answer that has been accepted. For A: Accessing UCSC mysql DB: ERROR 1045 (28000): Access denied for user 'genome'

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