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Post-imputation QC for input into GWAS analyses
gwas prs
updated 6 days ago by 4.2k • written 6 days ago by ▴ 100
1
vote
3
replies
616
views
No valid chromosomes found! on Michigan Imputation Server
michigan-imputation-server
updated 6 months ago by ★ 2.5k • written 6 months ago by ▴ 100
1
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0
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616
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Answer: Answer: No valid chromosomes found! on Michigan Imputation Server
6 months ago by graeme.thorn ▴ 100
0
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0
replies
616
views
Comment: Comment: No valid chromosomes found! on Michigan Imputation Server
6 months ago by graeme.thorn ▴ 100
0
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0
replies
566
views
Comment: Comment: Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
7 months ago by graeme.thorn ▴ 100
2
votes
2
replies
566
views
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
imputation
7 months ago by graeme.thorn ▴ 100
0
votes
1
reply
646
views
Comment: Comment: Michigan Imputation Server low reference overlap
8 months ago by graeme.thorn ▴ 100
0
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3
replies
646
views
Michigan Imputation Server low reference overlap
imputation michigan
updated 8 months ago by ★ 2.5k • written 8 months ago by ▴ 100
0
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0
replies
585
views
Comment: Comment: Skewed qq plot from logistic regression
9 months ago by graeme.thorn ▴ 100
0
votes
2
replies
585
views
Skewed qq plot from logistic regression
R glm qqplot
9 months ago by graeme.thorn ▴ 100
1
vote
0
replies
1.0k
views
Comment: Comment: write output files with default name
11 months ago by graeme.thorn ▴ 100
1
vote
1
reply
500
views
Normalise tab-delimited format to annovar input
annovar
18 months ago by graeme.thorn ▴ 100
1
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0
replies
500
views
Answer: Answer: Normalise tab-delimited format to annovar input
18 months ago by graeme.thorn ▴ 100
0
votes
2
replies
1.1k
views
Easy comparison between Whippet, SplAdder and DExSeq differential splicing analyses
SplAdder DExSeq splicing Whippet
updated 22 months ago by ▴ 20 • written 2.6 years ago by ▴ 100
0
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1
reply
1.4k
views
Comment: Comment: Hard filtering on GATK HaplotypeCaller giving multiple warnings
2.1 years ago by graeme.thorn ▴ 100
0
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3
replies
1.4k
views
Hard filtering on GATK HaplotypeCaller giving multiple warnings
haplotypecaller gatk warnings
updated 2.1 years ago by ▴ 830 • written 2.1 years ago by ▴ 100
0
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0
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1.4k
views
Answer: Answer: Hard filtering on GATK HaplotypeCaller giving multiple warnings
2.1 years ago by graeme.thorn ▴ 100
0
votes
0
replies
361
views
Systematic detection of transcript usage from Whippet results
whippet
2.3 years ago by graeme.thorn ▴ 100
1
vote
4
replies
1.1k
views
Extracting ENST ids from coordinates
biomart whippet
2.4 years ago by graeme.thorn ▴ 100
1
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0
replies
1.1k
views
Answer: Answer: Extracting ENST ids from coordinates
2.4 years ago by graeme.thorn ▴ 100
0
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1
reply
1.1k
views
Comment: Comment: Extracting ENST ids from coordinates
2.5 years ago by graeme.thorn ▴ 100
0
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0
replies
1.1k
views
Comment: Comment: Easy comparison between Whippet, SplAdder and DExSeq differential splicing analy
2.5 years ago by graeme.thorn ▴ 100
0
votes
2
replies
698
views
Prevent DEXSeq breaking transcripts entry when outputting to file
R DExSeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 100
0
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1
reply
1.4k
views
Comment: Comment: Intersecting compressed gVCF with bed file
2.7 years ago by graeme.thorn ▴ 100
0
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3
replies
1.4k
views
Intersecting compressed gVCF with bed file
bedtools gVCF intersect
updated 2.7 years ago by 161k • written 2.7 years ago by ▴ 100
0
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1
reply
1.3k
views
Comment: Comment: Consensus deduplication issues with non-matching/'slippy' primers?
3.0 years ago by graeme.thorn ▴ 100
0
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1
reply
1.3k
views
Comment: Comment: Consensus deduplication issues with non-matching/'slippy' primers?
3.0 years ago by graeme.thorn ▴ 100
0
votes
5
replies
1.3k
views
Consensus deduplication issues with non-matching/'slippy' primers?
DNA-seq deduplication
updated 3.0 years ago by 19k • written 3.1 years ago by ▴ 100
0
votes
0
replies
780
views
How to interpret output of SAM/SAMseq in R (samr package)
R
updated 3.2 years ago by 20 • written 3.2 years ago by ▴ 100
1
vote
2
replies
995
views
Variant data from covid-19 patients
covid-19 vcf
updated 3.3 years ago by 23k • written 4.0 years ago by ▴ 100
0
votes
0
replies
1.0k
views
MSigDB gmt files with Ensembl ID identifiers
msigdb
updated 3.4 years ago by 20 • written 3.5 years ago by ▴ 100
0
votes
1
reply
1.4k
views
Comment: C: Mutation calling directly from FASTQ files
3.5 years ago by graeme.thorn ▴ 100
2
votes
4
replies
1.4k
views
Mutation calling directly from FASTQ files
DNA-Seq variant calling
updated 3.5 years ago by 47k • written 3.5 years ago by ▴ 100
1
vote
1
reply
1.0k
views
PCA on exon count data
RNA-Seq R splicing
3.6 years ago by graeme.thorn ▴ 100
7
votes
7
replies
7.9k
views
Downloading hg38 centromere and telomere positions from UCSC table browser
ucsc R genome
updated 2.5 years ago by 11k • written 4.1 years ago by ▴ 100
0
votes
3
replies
843
views
Fixing genotypes from split vcf
vcf
3.9 years ago by graeme.thorn ▴ 100
0
votes
0
replies
1.5k
views
Comment: C: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
3.9 years ago by graeme.thorn ▴ 100
0
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0
replies
1.5k
views
Answer: A: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
3.9 years ago by graeme.thorn ▴ 100
0
votes
3
replies
1.5k
views
GATK VariantFiltration multiple filters including genotype for multi-sample VCF
vcf gatk
3.9 years ago by graeme.thorn ▴ 100
0
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0
replies
1.3k
views
Comment: C: RNAseq and PAM50 prediction
4.0 years ago by graeme.thorn ▴ 100
0
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2
replies
1.3k
views
RNAseq and PAM50 prediction
RNA-Seq R genefu
updated 4.0 years ago by 88k • written 4.0 years ago by ▴ 100
0
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0
replies
7.9k
views
Comment: C: Downloading hg38 centromere and telomere positions from UCSC table browser
4.1 years ago by graeme.thorn ▴ 100
1
vote
1
reply
887
views
Extracting variant reads and reference reads quickly from mapped files
dna-seq variant
4.2 years ago by graeme.thorn ▴ 100
0
votes
0
replies
899
views
Add signatures (trinucleotide context) to vcf file
variants
4.3 years ago by graeme.thorn ▴ 100
3
votes
1
reply
2.5k
views
ctDNA WES duplication rates from NovaSeq 6000 and HiSeq 4000
wes sequencing illumina novaseq
4.4 years ago by graeme.thorn ▴ 100
1
vote
1
reply
910
views
Generating a PoN with GATK CombineVariants using wildcards
vcf gatk
4.6 years ago by graeme.thorn ▴ 100
1
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0
replies
910
views
Answer: A: Generating a PoN with GATK CombineVariants using wildcards
4.6 years ago by graeme.thorn ▴ 100
0
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0
replies
3.4k
views
Comment: C: Understanding columns of ChIP-Seq BED file format
4.7 years ago by graeme.thorn ▴ 100
0
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0
replies
3.9k
views
Comment: C: Consensus reads from UMIs
4.7 years ago by graeme.thorn ▴ 100
4
votes
4
replies
3.9k
views
Consensus reads from UMIs
deduplication UMI DNA-seq
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 100
86 results • Page 1 of 2
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