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4
votes
1
reply
246
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 7 days ago by
zx8754
11k • written 9 days ago by
Jautis
▴ 560
3
votes
0
replies
246
views
Answer:
Answer: LD-prune variants while maintaining a list of SNPs
8 days ago by
Jautis
▴ 560
0
votes
0
replies
237
views
Troubleshooting error with BSmooth: `error in serialize(data, node$con)`
message
methylation
sequencing
R
error
3 months ago by
Jautis
▴ 560
0
votes
0
replies
316
views
Comment:
Comment: Match variants for allele frequency, LD score, and other features
5 months ago by
Jautis
▴ 560
0
votes
0
replies
581
views
Comment:
Comment: bcftools mipileup error: format error, unexpected A at line 1
6 months ago by
Jautis
▴ 560
1
vote
0
replies
512
views
Answer:
Answer: improving genome sequence read depth and confidence by combining sequences from
6 months ago by
Jautis
▴ 560
1
vote
1
reply
316
views
Match variants for allele frequency, LD score, and other features
snp
5 months ago by
Jautis
▴ 560
0
votes
6
replies
2.5k
views
Getting matrix of QDs from VCF file
vcf
snp
updated 14 months ago by
wlei091226
• 0 • written 7.6 years ago by
Jautis
▴ 560
2
votes
1
reply
420
views
Extract read position where a base is covered, and the allele at that base
samtools
bam
bwa
updated 10 months ago by
Ram
43k • written 18 months ago by
Jautis
▴ 560
0
votes
0
replies
14k
views
Comment:
Comment: How to download dbSNP153 vcf files in hg19/GRCH37 version
18 months ago by
Jautis
▴ 560
0
votes
1
reply
450
views
Extract mapped SE and properly paired PE reads from a bam file
properly
single
bam
end
mapped
paired
updated 23 months ago by
jv
★ 1.8k • written 23 months ago by
Jautis
▴ 560
0
votes
1
reply
991
views
Answer:
Answer: My PCA plot looks good but i don't have differentially expressed genes
2.2 years ago by
Jautis
▴ 560
2
votes
0
replies
937
views
Comment:
Comment: Should I normalize the data before or after filtering to a particular cell type?
2.2 years ago by
Jautis
▴ 560
4
votes
0
replies
656
views
Comment:
Comment: Differntial Gene Expression analysis
2.2 years ago by
Jautis
▴ 560
0
votes
0
replies
668
views
Comment:
Comment: SNPs with multiple nucleotides
2.2 years ago by
Jautis
▴ 560
2
votes
1
reply
668
views
Answer:
Answer: SNPs with multiple nucleotides
2.2 years ago by
Jautis
▴ 560
0
votes
1
reply
636
views
Comment:
Comment: Capture Hi-C processing yields sparse matrices
2.2 years ago by
Jautis
▴ 560
0
votes
0
replies
866
views
Comment:
Comment: Alternatives to TMM normalization
2.2 years ago by
Jautis
▴ 560
7
votes
4
replies
866
views
Alternatives to TMM normalization
voom
expression
R
limma
2.2 years ago by
Jautis
▴ 560
1
vote
0
replies
3.4k
views
Answer:
Answer: How can I colour UMAP by sample batches
2.3 years ago by
Jautis
▴ 560
0
votes
0
replies
1.5k
views
Comment:
Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.3 years ago by
Jautis
▴ 560
0
votes
0
replies
676
views
Comment:
Comment: Can I do differential analysis without phenodata?
2.3 years ago by
Jautis
▴ 560
3
votes
1
reply
943
views
Answer:
Answer: mutation not in RNAseq read
2.3 years ago by
Jautis
▴ 560
1
vote
1
reply
1.5k
views
Comment:
Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.3 years ago by
Jautis
▴ 560
0
votes
0
replies
1.9k
views
Comment:
Comment: Merge two vcf's, keep only intersection of REF/ALT alleles
2.3 years ago by
Jautis
▴ 560
0
votes
0
replies
372
views
Using bcftools to merge files of different individuals, getting only shared sites
vcf
genotypes
bcftools
2.3 years ago by
Jautis
▴ 560
1
vote
2
replies
1.5k
views
Answer:
Answer: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.3 years ago by
Jautis
▴ 560
2
votes
3
replies
1.3k
views
Error running smartpca from eigensoft: failed to create thread
pca
genotypes
smartpca
eigensoft
2.4 years ago by
Jautis
▴ 560
1
vote
0
replies
1.3k
views
Comment:
Comment: Error running smartpca from eigensoft: failed to create thread
2.4 years ago by
Jautis
▴ 560
0
votes
1
reply
1.3k
views
Comment:
Comment: Error running smartpca from eigensoft: failed to create thread
2.4 years ago by
Jautis
▴ 560
1
vote
0
replies
817
views
Comment:
Comment: Finding a sequence
2.4 years ago by
Jautis
▴ 560
1
vote
1
reply
4.4k
views
Comment:
Comment: fastqc html file
2.4 years ago by
Jautis
▴ 560
0
votes
1
reply
4.3k
views
Comment:
Comment: multiqc could not generate results
2.4 years ago by
Jautis
▴ 560
0
votes
0
replies
889
views
Comment:
Comment: Conserved regions in multiple fasta files (multiple species)?
2.4 years ago by
Jautis
▴ 560
0
votes
0
replies
4.4k
views
Comment:
Comment: fastqc html file
2.4 years ago by
Jautis
▴ 560
2
votes
2
replies
1.1k
views
Trim 100bp PE sequencing to 50bp reads
unix
bash
sequencing
fastq
updated 2.5 years ago by
cpad0112
21k • written 2.5 years ago by
Jautis
▴ 560
0
votes
0
replies
1.2k
views
Comment:
Comment: Bam file: replace low quality bases with "N"
2.6 years ago by
Jautis
▴ 560
2
votes
2
replies
1.2k
views
Bam file: replace low quality bases with "N"
quality
base
bam
2.6 years ago by
Jautis
▴ 560
0
votes
1
reply
1.7k
views
Comment:
Comment: limma+voom flips the sign of the effect from CPM?
2.6 years ago by
Jautis
▴ 560
1
vote
4
replies
1.7k
views
limma+voom flips the sign of the effect from CPM?
voom
expression
limma
R
updated 2.6 years ago by
Gordon Smyth
★ 7.1k • written 2.6 years ago by
Jautis
▴ 560
0
votes
1
reply
1.7k
views
Comment:
Comment: voom mean-variance plot has set of genes where variance increases with expressio
2.6 years ago by
Jautis
▴ 560
0
votes
1
reply
1.7k
views
Comment:
Comment: voom mean-variance plot has set of genes where variance increases with expressio
2.6 years ago by
Jautis
▴ 560
5
votes
5
replies
1.7k
views
voom mean-variance plot has set of genes where variance increases with expression level
voom
expression
limma
R
updated 2.6 years ago by
Gordon Smyth
★ 7.1k • written 2.6 years ago by
Jautis
▴ 560
0
votes
0
replies
2.3k
views
Comment:
Comment: unable to impute with beagle after filtering VCF table using vcftools
3.0 years ago by
Jautis
▴ 560
1
vote
1
reply
2.3k
views
Comment:
Comment: unable to impute with beagle after filtering VCF table using vcftools
3.0 years ago by
Jautis
▴ 560
0
votes
0
replies
996
views
Comment:
Comment: Could someone help me check what genomic position is this variant nomenclature r
3.0 years ago by
Jautis
▴ 560
0
votes
1
reply
3.1k
views
Comment:
Comment: How to calculate percent coverage of each read for nanopore
3.0 years ago by
Jautis
▴ 560
1
vote
0
replies
3.1k
views
Comment:
Comment: How to calculate percent coverage of each read for nanopore
3.0 years ago by
Jautis
▴ 560
0
votes
0
replies
1.8k
views
Comment:
Comment: Cannot color cells with 0 expression in certain color
3.0 years ago by
Jautis
▴ 560
0
votes
0
replies
591
views
Calculating Fst from low coverage data using genotype likelihoods
vcftools
fst
population_differentiation
3.0 years ago by
Jautis
▴ 560
152 results • Page
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