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Good quality control metrics to look out for when someone gives you BAMs
bam qc
5.7 years ago by curious ▴ 900
0
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0
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3.3k
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Comment: C: filter VCF based on info field that has a key but no value
5.7 years ago by curious ▴ 900
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0
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3.3k
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Comment: C: filter VCF based on info field that has a key but no value
5.7 years ago by curious ▴ 900
1
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0
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1.6k
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Comment: C: Genetic map for chromosome X that shows recombination rates?
5.7 years ago by curious ▴ 900
1
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2
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1.6k
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Genetic map for chromosome X that shows recombination rates?
shapeit phasing
updated 5.7 years ago by 89k • written 5.7 years ago by ▴ 900
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0
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5.9k
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Comment: C: update-chr issues with PLINK 1.9
5.7 years ago by curious ▴ 900
0
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1
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5.9k
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Comment: C: update-chr issues with PLINK 1.9
5.7 years ago by curious ▴ 900
1
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0
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3.4k
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Comment: A: Laptop specs for Bioinformatic analyses
5.7 years ago by curious ▴ 900
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0
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1.1k
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Trouble understanding Eagle2 phasing software "--allowRefAltSwap" flag
eagle phasing
5.7 years ago by curious ▴ 900
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0
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1.4k
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Comment: C: A2 different between PLINK .bim file and .frq file?
5.8 years ago by curious ▴ 900
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0
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1.9k
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Comment: C: ImportError: No module named cutadapt.scripts
5.8 years ago by curious ▴ 900
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2
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1.4k
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A2 different between PLINK .bim file and .frq file?
plink
updated 5.8 years ago by 11k • written 5.8 years ago by ▴ 900
0
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0
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1.7k
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Evaluating switch error rate when phasing with Eagle2?
phasing gwas eagle beagle
5.8 years ago by curious ▴ 900
0
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0
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1.4k
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When using Eagle, is the X chromosome typically phased without including pseudoautosomal regions?
eagle phasing
5.8 years ago by curious ▴ 900
0
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0
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3.0k
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Comment: C: Is there a way to force a specific order for variants in a PLINK file that have
5.8 years ago by curious ▴ 900
0
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1
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3.0k
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Comment: C: Is there a way to force a specific order for variants in a PLINK file that have
5.8 years ago by curious ▴ 900
0
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4
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3.0k
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Is there a way to force a specific order for variants in a PLINK file that have the same chromosome and bp position?
plink vcf
updated 5.8 years ago by 11k • written 5.8 years ago by ▴ 900
1
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1
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1.9k
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Comment: C: How to assign keys and values in a directory by using python
5.8 years ago by curious ▴ 900
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0
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1.0k
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bcftools error when re-annotating the FILTER column of a VCF when multiple ";" delimited FILTER values exist
vcf vcftools bcftools
5.9 years ago by curious ▴ 900
0
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1
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10k
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Comment: C: Why would you need to specify `--keep-allele-order` and `--a2-allele` when writi
5.9 years ago by curious ▴ 900
0
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1
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10k
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Comment: C: Why would you need to specify `--keep-allele-order` and `--a2-allele` when writi
5.9 years ago by curious ▴ 900
0
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0
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10k
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Comment: C: Why would you need to specify `--keep-allele-order` and `--a2-allele` when writi
5.9 years ago by curious ▴ 900
10
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9
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10k
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Why would you need to specify `--keep-allele-order` and `--a2-allele` when writing a VCF with PLINK?
plink vcf
updated 3.9 years ago by ★ 9.6k • written 5.9 years ago by ▴ 900
0
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0
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5.0k
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Comment: C: Are there any GenomeStudio alternatives to process Illumina genotyping array?
6.0 years ago by curious ▴ 900
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0
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2.2k
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Comment: C: bcftools view -Oz -S [sample list] [input vcf] -o [output vcf] incredibly slow f
6.0 years ago by curious ▴ 900
0
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2
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2.2k
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bcftools view -Oz -S [sample list] [input vcf] -o [output vcf] incredibly slow for vcf with many samples
vcf bcftools
updated 6.0 years ago by 166k • written 6.0 years ago by ▴ 900
2
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0
replies
11k
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Comment: C: theta value and R value in SNP data
6.1 years ago by curious ▴ 900
0
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1
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1.5k
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Comment: C: Question about why Illumina HumanExome SNP arrays appear to detect [A/T] and [C/
6.1 years ago by curious ▴ 900
0
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3
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1.5k
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Question about why Illumina HumanExome SNP arrays appear to detect [A/T] and [C/G] SNPs by using two different probes.
SNP gwas illumina array
updated 6.1 years ago by 89k • written 6.1 years ago by ▴ 900
0
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2
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1.7k
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How does genenomestudio's genotyping module calculate minor allele frequency (Minor Freq)?
genomestudio maf SNP gwas
updated 6.1 years ago by 20 • written 6.1 years ago by ▴ 900
0
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0
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1.7k
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Comment: C: Are values from the within-family id column of a plink .fam file supposed to uni
6.1 years ago by curious ▴ 900
1
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2
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1.7k
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Are values from the within-family id column of a plink .fam file supposed to unique within just the family or within the whole dataset?
plink gwas
6.1 years ago by curious ▴ 900
1
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0
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117k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
6.1 years ago by curious ▴ 900
0
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0
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1.7k
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Comment: C: How does genenomestudio's genotyping module calculate minor allele frequency (Mi
6.1 years ago by curious ▴ 900
0
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0
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10k
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Comment: C: Read binary Illumina GTC files (1000 genomes)
6.2 years ago by curious ▴ 900
0
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0
replies
11k
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Comment: C: Genomestudio: The Project Can Not Be Created. No Valid Samples Were Loaded
6.2 years ago by curious ▴ 900
0
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1
reply
5.0k
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Comment: C: Are there any GenomeStudio alternatives to process Illumina genotyping array?
6.2 years ago by curious ▴ 900
0
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0
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4.3k
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Comment: A: Assistance with coxph and standard errors
6.2 years ago by curious ▴ 900
0
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1
reply
2.7k
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Comment: C: variant calling using pseudoaligners
6.2 years ago by curious ▴ 900
0
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0
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1.5k
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Comment: C: Libre office in ubuntu is changing my gene names to dates
6.3 years ago by curious ▴ 900
0
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1
reply
2.6k
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Comment: C: Question about implementing quality control of TCGA data for survival analysis
6.3 years ago by curious ▴ 900
0
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0
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2.6k
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Comment: C: Question about implementing quality control of TCGA data for survival analysis
6.3 years ago by curious ▴ 900
0
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0
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2.6k
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Comment: C: Question about implementing quality control of TCGA data for survival analysis
6.3 years ago by curious ▴ 900
0
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6
replies
2.6k
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Question about implementing quality control of TCGA data for survival analysis
survival cox regression tcga
updated 6.3 years ago by ▴ 170 • written 6.3 years ago by ▴ 900
3
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0
replies
6.0k
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Answer: Answer: Bioinformatics Workstation Suggestions
6.4 years ago by curious ▴ 900
0
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0
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1.9k
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Comment: C: how to download pubmed article abstracts for multiple terms using programming?
6.5 years ago by curious ▴ 900
1
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0
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1.3k
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Comment: C: Extract and ADD text information
6.5 years ago by curious ▴ 900
1
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0
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4.0k
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Can two Kaplan-Meier survival curves cross and still have proportional hazards?
cox regression survival
6.5 years ago by curious ▴ 900
2
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0
replies
3.1k
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Answer: A: How to select only protein coding mRNAs from a really long list of ENSG IDS
6.5 years ago by curious ▴ 900
3
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2
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3.1k
views
How to select only protein coding mRNAs from a really long list of ENSG IDS
ensg ensembl ids rna
6.5 years ago by curious ▴ 900
316 results • Page 6 of 7
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