User: Mr Locuace

gravatar for Mr Locuace
Mr Locuace90
Reputation:
90
Status:
Trusted
Location:
Chile
Last seen:
1 day, 3 hours ago
Joined:
3 years, 11 months ago
Email:
l*******@gmail.com

Molecular biologist by training that recently joined a Human Genomics group.

Posts by Mr Locuace

<prev • 57 results • page 1 of 6 • next >
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Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
... Thank you very much @ATpoint ! ...
written 10 weeks ago by Mr Locuace90
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Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
... Thank you @Sean Davis !. But what about the single file that says "PAIRED"?. How to know if it is actually single-end or a merge between read1 and read2 paired-ends? ...
written 10 weeks ago by Mr Locuace90
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ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.gz X_2.fastq.gz
... Hello, I am downloading some data from this project from ENA: https://www.ebi.ac.uk/ena/data/search?query=PRJNA494719 There are cases where I do not understand the format. For instance, this is supposed to be a single-end file (it says "SINGLE"): https://www.ebi.ac.uk/ena/data/view/SRX4809217 bu ...
fastq paired-end single-end ena written 10 weeks ago by Mr Locuace90 • updated 10 weeks ago by Sean Davis25k
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Convert from plink or vcf to bgl format
... Hello, I'd like to convert a vcf or bed/bim/fam file to Beagle (.bgl) format. Thanks ! ...
vcf bgl plink written 11 weeks ago by Mr Locuace90
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Convert physical positions from Hg18 to Hg19
... Hello, I have a file like this one (but with thousands of rows): A B C D 994 437756 1 437756 988 204037 1 641793 982 89637 1 731430 976 48461 1 779891 970 30768 1 810659 964 21334 1 831993 A: score B: size of the genomic region in base pairs C: chromosome ...
liftover written 4 months ago by Mr Locuace90 • updated 4 months ago by ATpoint24k
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Phasing genotype likelihood data and merging them with phased genotype calls data.
... I have 3 sets of genotypes: 1. A multiethnic panel of phased 1000G Phase 3 genotypes in IMPUTE2 format (.hap). 2. Genotype likelihoods (GL) for 40 whole-genotypes of a population A in .vcf format (field FORMAT=GL) 3. An array of about 600.000 SNP (30X coverage) from a population B, which is geneti ...
genotype likelihood phasing genotype calls written 6 months ago by Mr Locuace90
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Plink2. psam file missing in 1000G Phase3
... Hello, here there is a merged file with all 1000G Phase3 chromosomes: https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 They provide the .pgen.zst, .pvar.zst and unannotated .pvar.zst files, but no -psam.zst file. Is there any way to create a psam file out of the two former files, so I ...
plink2 written 8 months ago by Mr Locuace90 • updated 8 months ago by chrchang5235.6k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Thanks so much for this tutorial, Kevin !! ...
written 8 months ago by Mr Locuace90
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Get all SNPs that are in high linkage disequilibrium (based on D') for a set of SNPs
... Hello, I have phased plink files of a population. I would like to obtain all SNPs that are in high linkage disequilibrium (LD) for a set of 10 SNPs. I know how to do it according to a r2 threshold, but I need to set this threshold according to D' For instance, this script will output all variants i ...
snp plink ld written 8 months ago by Mr Locuace90 • updated 8 months ago by chrchang5235.6k
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Answer: A: How to calculate Hudson's Fst at Population and SNP level?
... https://www.rdocumentation.org/packages/KRIS/versions/1.1.1/topics/fst.each.snp.hudson ...
written 11 months ago by Mr Locuace90

Latest awards to Mr Locuace

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Voter 5 months ago, voted more than 100 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 11 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 12 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 13 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Popular Question 13 months ago, created a question with more than 1,000 views. For Lift over based on physical position from GRCh37 build 137 to GRCh37 build 132
Popular Question 19 months ago, created a question with more than 1,000 views. For Getting derived alleles from alternate/reference allele data
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Reference & alternative alleles extracted from 1000G, Phase 3
Scholar 20 months ago, created an answer that has been accepted. For A: Reference & alternative alleles extracted from 1000G, Phase 3
Supporter 3.4 years ago, voted at least 25 times.
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

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