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4
votes
1
reply
378
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 4 months ago by 12k • written 4 months ago by ▴ 580
3
votes
0
replies
378
views
Answer: Answer: LD-prune variants while maintaining a list of SNPs
4 months ago by Jautis ▴ 580
0
votes
0
replies
335
views
Troubleshooting error with BSmooth: `error in serialize(data, node$con)`
R sequencing methylation bsseq
updated 12 weeks ago by 44k • written 7 months ago by ▴ 580
0
votes
0
replies
385
views
Comment: Comment: Match variants for allele frequency, LD score, and other features
9 months ago by Jautis ▴ 580
0
votes
0
replies
728
views
Comment: Comment: bcftools mipileup error: format error, unexpected A at line 1
10 months ago by Jautis ▴ 580
1
vote
0
replies
630
views
Answer: Answer: improving genome sequence read depth and confidence by combining sequences from
10 months ago by Jautis ▴ 580
1
vote
1
reply
385
views
Match variants for allele frequency, LD score, and other features
snp
9 months ago by Jautis ▴ 580
0
votes
6
replies
2.6k
views
Getting matrix of QDs from VCF file
vcf snp
updated 18 months ago by • 0 • written 7.9 years ago by ▴ 580
2
votes
1
reply
464
views
Extract read position where a base is covered, and the allele at that base
samtools bam bwa
updated 15 months ago by 44k • written 22 months ago by ▴ 580
0
votes
0
replies
15k
views
Comment: Comment: How to download dbSNP153 vcf files in hg19/GRCH37 version
22 months ago by Jautis ▴ 580
0
votes
1
reply
524
views
Extract mapped SE and properly paired PE reads from a bam file
properly single bam end mapped paired
updated 2.3 years ago by ★ 1.8k • written 2.3 years ago by ▴ 580
0
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1
reply
1.1k
views
Answer: Answer: My PCA plot looks good but i don't have differentially expressed genes
2.5 years ago by Jautis ▴ 580
2
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0
replies
1.1k
views
Comment: Comment: Should I normalize the data before or after filtering to a particular cell type?
2.5 years ago by Jautis ▴ 580
4
votes
0
replies
729
views
Comment: Comment: Differntial Gene Expression analysis
2.5 years ago by Jautis ▴ 580
0
votes
0
replies
781
views
Comment: Comment: SNPs with multiple nucleotides
2.5 years ago by Jautis ▴ 580
2
votes
1
reply
781
views
Answer: Answer: SNPs with multiple nucleotides
2.5 years ago by Jautis ▴ 580
0
votes
1
reply
761
views
Comment: Comment: Capture Hi-C processing yields sparse matrices
2.5 years ago by Jautis ▴ 580
0
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0
replies
999
views
Comment: Comment: Alternatives to TMM normalization
2.5 years ago by Jautis ▴ 580
7
votes
4
replies
999
views
Alternatives to TMM normalization
voom expression R limma
2.5 years ago by Jautis ▴ 580
1
vote
0
replies
3.9k
views
Answer: Answer: How can I colour UMAP by sample batches
2.7 years ago by Jautis ▴ 580
0
votes
0
replies
1.7k
views
Comment: Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.7 years ago by Jautis ▴ 580
0
votes
0
replies
766
views
Comment: Comment: Can I do differential analysis without phenodata?
2.7 years ago by Jautis ▴ 580
3
votes
1
reply
1.0k
views
Answer: Answer: mutation not in RNAseq read
2.7 years ago by Jautis ▴ 580
1
vote
1
reply
1.7k
views
Comment: Comment: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.7 years ago by Jautis ▴ 580
0
votes
0
replies
2.1k
views
Comment: Comment: Merge two vcf's, keep only intersection of REF/ALT alleles
2.7 years ago by Jautis ▴ 580
0
votes
0
replies
427
views
Using bcftools to merge files of different individuals, getting only shared sites
vcf genotypes bcftools
2.7 years ago by Jautis ▴ 580
1
vote
2
replies
1.7k
views
Answer: Answer: single cell RNA-seq: Is there a way to tell if one dataset is more similar to an
2.7 years ago by Jautis ▴ 580
2
votes
3
replies
1.4k
views
Error running smartpca from eigensoft: failed to create thread
pca genotypes smartpca eigensoft
2.8 years ago by Jautis ▴ 580
1
vote
0
replies
1.4k
views
Comment: Comment: Error running smartpca from eigensoft: failed to create thread
2.8 years ago by Jautis ▴ 580
0
votes
1
reply
1.4k
views
Comment: Comment: Error running smartpca from eigensoft: failed to create thread
2.8 years ago by Jautis ▴ 580
1
vote
0
replies
884
views
Comment: Comment: Finding a sequence
2.8 years ago by Jautis ▴ 580
1
vote
1
reply
5.0k
views
Comment: Comment: fastqc html file
2.8 years ago by Jautis ▴ 580
0
votes
1
reply
4.6k
views
Comment: Comment: multiqc could not generate results
2.8 years ago by Jautis ▴ 580
0
votes
0
replies
998
views
Comment: Comment: Conserved regions in multiple fasta files (multiple species)?
2.8 years ago by Jautis ▴ 580
0
votes
0
replies
5.0k
views
Comment: Comment: fastqc html file
2.8 years ago by Jautis ▴ 580
2
votes
2
replies
1.3k
views
Trim 100bp PE sequencing to 50bp reads
unix bash sequencing fastq
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 580
0
votes
0
replies
1.3k
views
Comment: Comment: Bam file: replace low quality bases with "N"
2.9 years ago by Jautis ▴ 580
2
votes
2
replies
1.3k
views
Bam file: replace low quality bases with "N"
quality base bam
2.9 years ago by Jautis ▴ 580
0
votes
1
reply
1.8k
views
Comment: Comment: limma+voom flips the sign of the effect from CPM?
3.0 years ago by Jautis ▴ 580
1
vote
4
replies
1.8k
views
limma+voom flips the sign of the effect from CPM?
voom expression limma R
updated 3.0 years ago by ★ 7.3k • written 3.0 years ago by ▴ 580
0
votes
1
reply
2.0k
views
Comment: Comment: voom mean-variance plot has set of genes where variance increases with expressio
3.0 years ago by Jautis ▴ 580
0
votes
1
reply
2.0k
views
Comment: Comment: voom mean-variance plot has set of genes where variance increases with expressio
3.0 years ago by Jautis ▴ 580
6
votes
5
replies
2.0k
views
voom mean-variance plot has set of genes where variance increases with expression level
voom expression limma R
updated 3.0 years ago by ★ 7.3k • written 3.0 years ago by ▴ 580
0
votes
0
replies
2.5k
views
Comment: Comment: unable to impute with beagle after filtering VCF table using vcftools
3.4 years ago by Jautis ▴ 580
1
vote
1
reply
2.5k
views
Comment: Comment: unable to impute with beagle after filtering VCF table using vcftools
3.4 years ago by Jautis ▴ 580
0
votes
0
replies
1.1k
views
Comment: Comment: Could someone help me check what genomic position is this variant nomenclature r
3.4 years ago by Jautis ▴ 580
0
votes
1
reply
3.3k
views
Comment: Comment: How to calculate percent coverage of each read for nanopore
3.4 years ago by Jautis ▴ 580
1
vote
0
replies
3.3k
views
Comment: Comment: How to calculate percent coverage of each read for nanopore
3.4 years ago by Jautis ▴ 580
0
votes
0
replies
2.0k
views
Comment: Comment: Cannot color cells with 0 expression in certain color
3.4 years ago by Jautis ▴ 580
1
vote
0
replies
651
views
Calculating Fst from low coverage data using genotype likelihoods
vcftools fst population_differentiation
3.4 years ago by Jautis ▴ 580
152 results • Page 1 of 4
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