User: magda.meier

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magda.meier20
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Posts by magda.meier

<prev • 11 results • page 1 of 2 • next >
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Problem imputing (large) file into GenABEL
... I have a very large imputation file (363GB in total) so I need to convert to a filevector format with GenABEL. My imputation file is in IMPUTE2 format and looks like so standard .imputed file: 21 rs142159069 45000079 T T 1 0 0 etc etc In other words, each row is a SNP with colu ...
impute2databel impute2 genabel written 5 weeks ago by magda.meier20
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IMPUTE2: change names of specific SNPs
... I have some files generated through IMPUTE2. They all look like so: --- 8:50000031:C:T 50000031 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 --- 8:50000032:G:A 50000032 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 Associated with each file, I have a list of SNPs for which I would like to change the name. For example: ...
impute2 snps names written 8 weeks ago by magda.meier20
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Bash: find duplicates based on 2 columns and keep duplicate with lowest value in a different column
... I have a file like this: chr snpid position alleleA alleleB score chr1 id1 1720593 A T 2 chr4 id2 1795915 T A 2 chr9 id3 2405331 C G 0 chr10 id4 2791133 G C 1 chr11 id5 2849732 A C 2 chr13 id6 3220462 C A 4 chr19 id8 3278835 T A 3 chr19 id8 3278835 T A 4 I would ...
duplicates bash awk written 9 weeks ago by magda.meier20 • updated 9 weeks ago by shenwei3563.4k
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R: How to test for trend of risk scores
... I have some case/control data like so (many more rows) ID score phenotype 1 0.6482772 0 2 0.9519315 1 3 2.7689036 0 4 1.9974466 1 5 1.6287841 1 6 1.9993825 0 I performed a logistic regression ...
R trend test risk scores written 10 weeks ago by magda.meier20 • updated 10 weeks ago by Biostar ♦♦ 20
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Gtool missing output .sample file
... I am using Gtool to exclude some SNPs from a .imputed file. My command is as follows: /apps/gtool/0.7.5/gtool -S \ --g ../../../Imputation/chr10.11.imputed \ --s gwas_pheno.sample \ --og chr10.11.imputed.after_exclusion.imputed \ --os chr10.11.imputed.after_exclusion.sample \ ...
missing output file .sample file gtool written 11 weeks ago by magda.meier20
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Answer: A: Which skills are most required to become a good bioinformatician?
... Thanks to you all of you for your answers, that's really useful. Will definitely keep learning Python, R I know better but not in great depth (I still struggle while using specific rare packages). I also know Bash as I have to handle large datasets on the cluster. Thanks again! ...
written 11 weeks ago by magda.meier20
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Which skills are most required to become a good bioinformatician?
... I am half way through my PhD and I am considering pursuing a career in bioinformatics. My experience in bioinformatics is limited: I started coding 3 years ago but very slowly and my PhD is half bioinformatics half laboratory based. I currently have experience in bash and R. I am also trying to lear ...
improving career bioinformatics job education written 11 weeks ago by magda.meier20 • updated 5 weeks ago by Biostar ♦♦ 20
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Snptest -overlap option
... I am running Snptest on 2 datasets together. I used the -overlap option to make sure I tested only the SNPs common to both datasets. My code looks as follows: /apps/snptest/2.5.2/snptest_v2.5.2 \ -data data1.imputed pheno1.sample data2.imputed pheno2.sample \ -overlap \ -o combined.snptest \ -frequ ...
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Problem with PRSice package using dosage files
... I am trying to use the PRSice package to calculate a polygenic risk score for my group of samples. My input files are .imputed files (generated with IMPUTE2) that has been modified with bash to have dosage data. In other words, instead of looking like this (3 probabilities per SNP: AA,AB,BB) ...
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Comment: C: Confusing allele notation for SNP data
... My apologies. This SNP has indeed been imputed using Phase3 1000 Genomes data and the software IMPUTE2. To me this SNP appears to be a CNV and the nomenclature means that one allele is 0 and the other is , whatever this means. I am just quite confused because this SNP doesn't appear to be a CNV a ...
written 4 months ago by magda.meier20

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