User: magda.meier
magda.meier • 20
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Posts by magda.meier
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2
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... 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 ...
written 3 days ago by
magda.meier • 20
• updated
3 days ago by
shenwei356 • 3.3k
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... 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 ...
written 14 days ago by
magda.meier • 20
• updated
10 days ago by
Biostar ♦♦ 20
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... 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 \
...
written 16 days ago by
magda.meier • 20
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... 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 16 days ago by
magda.meier • 20
6
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8 follow
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... 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 ...
written 21 days ago by
magda.meier • 20
• updated
16 days ago by
theobroma22 • 930
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... 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 ...
written 28 days ago by
magda.meier • 20
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... 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)
...
written 9 weeks ago by
magda.meier • 20
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... 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 10 weeks ago by
magda.meier • 20
2
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... I am working on some imputed data and one of the SNPs I am interested in shows up after imputation as:
name position alleles
22:39359355:C::39379392 39359355 C CN0
I am confused as to what C CNO means. Is this a CNV or an indel?
Thanks ...
written 10 weeks ago by
magda.meier • 20
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