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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
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
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
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
7
votes
4
replies
999
views
Alternatives to TMM normalization
voom expression R limma
2.5 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
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
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
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
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
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
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
7
votes
15
replies
7.3k
views
6 follow
Modifying fasta file based on vcf information
reference-genome vcf fasta
updated 21 months ago by 44k • written 9.3 years ago by ▴ 580
0
votes
0
replies
655
views
GO based on NCBI annotation
genome enrichment GSEA GO
4.0 years ago by Jautis ▴ 580
0
votes
0
replies
1.2k
views
Convert VCF + LDhelmet Recombination Rates to EIGENSTRAT format
vcf linkage SNP genome
4.5 years ago by Jautis ▴ 580
0
votes
0
replies
1.1k
views
find position of snps in cM, given recombination map from ldhelmet
recombination genome physical position
4.5 years ago by Jautis ▴ 580
2
votes
2
replies
2.7k
views
sed (or similar) command to remove part of the FORMAT from a vcf file?
vcf sed processing
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 580
1
vote
2
replies
1.9k
views
vcftools minDP filter not working for samtools genotype calling output
genotype filtering SNP SNP-calling
4.9 years ago by Jautis ▴ 580
0
votes
1
reply
1.1k
views
Efficiently run blat for long sequences
blat alignment sequence assembly
updated 5.0 years ago by ★ 2.5k • written 5.0 years ago by ▴ 580
1
vote
1
reply
1.5k
views
Annotate CpG Islands for a new genome
CpG assembly annotation
updated 5.4 years ago by ★ 3.7k • written 5.4 years ago by ▴ 580
1
vote
8
replies
2.7k
views
Error in transferring annotations to a new assembly using RATT
alignment annotation software error Assembly
updated 5.6 years ago by 35k • written 5.7 years ago by ▴ 580
2
votes
1
reply
2.7k
views
Create a pseudo-haploid fasta file based genotype calls for an individual (vcf file)
vcf sequence assembly SNP
updated 5.8 years ago by ★ 1.6k • written 5.8 years ago by ▴ 580
0
votes
0
replies
1.1k
views
Find SNPs which disrupt CpG sites
vcf genome variants
5.9 years ago by Jautis ▴ 580
0
votes
0
replies
1.5k
views
Determine the derived allele
alignment
6.1 years ago by Jautis ▴ 580
1
vote
2
replies
2.8k
views
GOseq with non-supported organism
GO GOseq R
6.1 years ago by Jautis ▴ 580
1
vote
5
replies
1.6k
views
Find chromosomal location of a scaffold
genome mapping
updated 6.1 years ago by 35k • written 6.1 years ago by ▴ 580
3
votes
4
replies
3.9k
views
Convert an altered sam file into a bam file
sam bam sequencing
6.7 years ago by Jautis ▴ 580
0
votes
0
replies
1.8k
views
BSMap to Bismark bam file formats
next-gen sequencing bam bisulfite
6.8 years ago by Jautis ▴ 580
0
votes
2
replies
1.3k
views
Genotype calls for a list of variable sites
genotype-calling GATK variant-calling
updated 6.9 years ago by 163k • written 6.9 years ago by ▴ 580
10
votes
4
replies
6.3k
views
Comparing two phylogenies
covariance phylogeny tree
updated 2.0 years ago by 44k • written 9.0 years ago by ▴ 580
2
votes
3
replies
2.0k
views
Outputting DP4 flag in GATK
variant calling sequencing gatk
updated 7.4 years ago by 5.8k • written 7.4 years ago by ▴ 580
0
votes
7
replies
1.7k
views
Getting reads that end at a digest site from a sam/bam file
bisulfite digest
updated 7.5 years ago by 163k • written 7.5 years ago by ▴ 580
0
votes
1
reply
1.9k
views
Calling allele-specific methylation from bisulfite sequencing reads
bisulfite-sequencing allele-specific sequencing
updated 7.6 years ago by 14k • written 7.6 years ago by ▴ 580
5
votes
7
replies
6.0k
views
Downsampling bam file to 2x coverage
bam sequencing high-throughput
7.7 years ago by Jautis ▴ 580
0
votes
1
reply
1.3k
views
high coverage but few genotype calls: possible causes?+
genotype calling sequencing SNP
8.3 years ago by Jautis ▴ 580
3
votes
4
replies
6.1k
views
Compare tree topologies (Newick)
tree phylogeny gene
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by ▴ 580
0
votes
1
reply
1.6k
views
Check for Msp1 digestion in sequencing data
RRBS digestion bisulfite-sequencing msp1
updated 2.1 years ago by 44k • written 8.7 years ago by ▴ 580
0
votes
0
replies
2.6k
views
Genome sites from BPM file
illumina location bpm
updated 2.1 years ago by 44k • written 8.8 years ago by ▴ 580
2
votes
2
replies
2.7k
views
Phylogenetic distance betwee species
phylogenetics newick trees
updated 2.1 years ago by 44k • written 8.8 years ago by ▴ 580
0
votes
2
replies
2.3k
views
Fst from 012 genotype matrix
Fst Genotype
updated 2.0 years ago by 44k • written 8.9 years ago by ▴ 580
2
votes
6
replies
3.7k
views
Taking genotypes out of a vcf file
vcf
updated 23 months ago by 44k • written 9.1 years ago by ▴ 580
4
votes
3
replies
2.3k
views
Making a haploid genome
vcf haploid-genome variant
updated 21 months ago by 44k • written 9.2 years ago by ▴ 580
0
votes
1
reply
2.6k
views
Masking Variable Sites in a Fasta File
fasta vcf
updated 21 months ago by 44k • written 9.2 years ago by ▴ 580
0
votes
1
reply
3.0k
views
Finding differences between 2 fasta files
fasta
updated 21 months ago by 44k • written 9.2 years ago by ▴ 580
6
votes
4
replies
2.7k
views
Help simulating RRBS reads
methylation RRBS
updated 20 months ago by 44k • written 9.3 years ago by ▴ 580
7
votes
5
replies
2.6k
views
Filter fastq file by first two base pairs
fastq
updated 20 months ago by 44k • written 9.3 years ago by ▴ 580
6
votes
2
replies
1.6k
views
Comparing methods to genotype
RNA-Seq genotyping vcf RRBS
updated 2.2 years ago by 44k • written 9.4 years ago by ▴ 580
1
vote
6
replies
3.4k
views
Calling SNPs from RRBS data
SNP RRBS SNP-calling bisulfite-sequencing
updated 2.4 years ago by 44k • written 9.6 years ago by ▴ 580
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