User: m93

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m9330
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Posts by m93

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NGS analysis: how to handle paired-end reads
... I am learning how to analyse NGS data. I have a data for 192 samples. These were obtained through a targeted sequencing library prep. I have 192 samples, but technically I have received 2 files for each sample. For example: - sample1_TTGCCTT_L008_R1_001.fastq.gz - sample1_TTGCCTT_L008_R2_001.f ...
ngs paired-end reads pipeline analysis written 8 weeks ago by m9330 • updated 8 weeks ago by manuel.belmadani30
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Comment: C: Definition of minor and major allele and connection with risk, effect, wildtype
... Thank you so much for clarifying all this for me! ...
written 8 weeks ago by m9330
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Comment: C: Definition of minor and major allele and connection with risk, effect, wildtype
... Thank you so much! I should have added "ancestral" allele in my question. Am I correct in saying the ancestral allele is the major allele, given a large reference population? ...
written 8 weeks ago by m9330
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Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
... In the context of genotype data and/or NGS datasets, could someone provide a clear definition and differences between minor, major, risk, reference, wildtype and effect alleles? I find terms are very often interchanged without a clear definition in various software. My current understand is as foll ...
alleles minor reference risk major written 8 weeks ago by m9330 • updated 8 weeks ago by Kevin Blighe21k
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Obtaining hazard ratio from beta and chi-square values
... I have used a program called Probabel to run a cox regression on genotype data (to look for association with disease status). My output file looks as follows contains beta_SNP_addA1, sebeta_SNP_addA1 and chi2_SNP_add. Is there any way I can use these values to obtain P-values and Hazard ratios? Ma ...
cox_regression hazard_ratio probabel written 6 months ago by m9330 • updated 6 months ago by Kevin Blighe21k
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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 8 months ago by m9330
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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 9 months ago by m9330
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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 months ago by m9330 • updated 9 months ago by shenwei3563.8k
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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 9 months ago by m9330 • updated 9 months 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 9 months ago by m9330

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Student 14 days ago, asked a question with at least 3 up-votes. For Which skills are most required to become a good bioinformatician?

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