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Answer: A: 012 genotype matrix using vcf tools
3.4 years ago by Jautis ▴ 530
7
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15
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7.0k
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6 follow
Modifying fasta file based on vcf information
reference-genome vcf fasta
updated 16 months ago by 43k • written 8.9 years ago by ▴ 530
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618
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GO based on NCBI annotation
genome enrichment GSEA GO
3.7 years ago by Jautis ▴ 530
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0
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1.2k
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Comment: C: Phasing non-human genomes with Beagle - do I need to divide subjects by populati
3.8 years ago by Jautis ▴ 530
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1
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13k
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Comment: C: How to remove a list of reads from fastq file?
3.9 years ago by Jautis ▴ 530
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1.2k
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Convert VCF + LDhelmet Recombination Rates to EIGENSTRAT format
vcf linkage SNP genome
4.1 years ago by Jautis ▴ 530
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0
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1.0k
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find position of snps in cM, given recombination map from ldhelmet
recombination genome physical position
4.1 years ago by Jautis ▴ 530
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2.3k
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Comment: C: sed (or similar) command to remove part of the FORMAT from a vcf file?
4.2 years ago by Jautis ▴ 530
2
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2
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2.3k
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sed (or similar) command to remove part of the FORMAT from a vcf file?
vcf sed processing
updated 4.2 years ago by 16k • written 4.2 years ago by ▴ 530
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1
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14k
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Comment: C: How to combine chromosome vcf files
4.2 years ago by Jautis ▴ 530
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2.6k
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Comment: C: Phylogenetic distance betwee species
updated 4.4 years ago by 43k • written 8.4 years ago by ▴ 530
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4.5k
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Comment: C: Good Bioinformatics research papers
updated 4.4 years ago by 43k • written 8.4 years ago by ▴ 530
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1
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3.5k
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Comment: C: Taking genotypes out of a vcf file
updated 4.5 years ago by 43k • written 8.7 years ago by ▴ 530
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0
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13k
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Comment: C: Calculating the bisulfite conversion rate
updated 4.5 years ago by 43k • written 8.8 years ago by ▴ 530
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2
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13k
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Answer: A: Calculating the bisulfite conversion rate
updated 4.5 years ago by 43k • written 8.8 years ago by ▴ 530
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0
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1.8k
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Comment: C: vcftools minDP filter not working for samtools genotype calling output
4.5 years ago by Jautis ▴ 530
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2
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1.8k
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vcftools minDP filter not working for samtools genotype calling output
genotype filtering SNP SNP-calling
4.5 years ago by Jautis ▴ 530
0
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1
reply
977
views
Efficiently run blat for long sequences
blat alignment sequence assembly
updated 4.6 years ago by ★ 2.5k • written 4.6 years ago by ▴ 530
1
vote
1
reply
1.4k
views
Annotate CpG Islands for a new genome
CpG assembly annotation
updated 5.0 years ago by ★ 3.7k • written 5.0 years ago by ▴ 530
1
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8
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2.5k
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Error in transferring annotations to a new assembly using RATT
alignment annotation software error Assembly
updated 5.2 years ago by 35k • written 5.3 years ago by ▴ 530
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2
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2.5k
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Comment: C: Error in transferring annotations to a new assembly using RATT
5.3 years ago by Jautis ▴ 530
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2
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2.5k
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Comment: C: Error in transferring annotations to a new assembly using RATT
5.3 years ago by Jautis ▴ 530
2
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1
reply
2.6k
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Create a pseudo-haploid fasta file based genotype calls for an individual (vcf file)
vcf sequence assembly SNP
updated 5.5 years ago by ★ 1.6k • written 5.5 years ago by ▴ 530
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0
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1.0k
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Find SNPs which disrupt CpG sites
vcf genome variants
5.5 years ago by Jautis ▴ 530
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0
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1.5k
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Determine the derived allele
alignment
5.7 years ago by Jautis ▴ 530
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0
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2.7k
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Comment: C: GOseq with non-supported organism
5.7 years ago by Jautis ▴ 530
1
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2
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2.7k
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GOseq with non-supported organism
GO GOseq R
5.7 years ago by Jautis ▴ 530
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1
reply
1.5k
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Comment: C: Find chromosomal location of a scaffold
5.8 years ago by Jautis ▴ 530
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1
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1.5k
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Comment: C: Find chromosomal location of a scaffold
5.8 years ago by Jautis ▴ 530
1
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5
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1.5k
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Find chromosomal location of a scaffold
genome mapping
updated 5.8 years ago by 35k • written 5.8 years ago by ▴ 530
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1
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3.7k
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Comment: C: Convert an altered sam file into a bam file
6.4 years ago by Jautis ▴ 530
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4
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3.7k
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Convert an altered sam file into a bam file
sam bam sequencing
6.4 years ago by Jautis ▴ 530
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0
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1.8k
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BSMap to Bismark bam file formats
next-gen sequencing bam bisulfite
6.4 years ago by Jautis ▴ 530
0
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0
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1.2k
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Comment: C: Genotype calls for a list of variable sites
6.5 years ago by Jautis ▴ 530
0
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2
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1.2k
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Genotype calls for a list of variable sites
genotype-calling GATK variant-calling
updated 6.5 years ago by 161k • written 6.5 years ago by ▴ 530
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0
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7.0k
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Comment: C: Modifying fasta file based on vcf information
6.9 years ago by Jautis ▴ 530
10
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4
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6.1k
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Comparing two phylogenies
covariance phylogeny tree
updated 19 months ago by 43k • written 8.6 years ago by ▴ 530
0
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1
reply
1.9k
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Comment: C: Outputting DP4 flag in GATK
7.1 years ago by Jautis ▴ 530
2
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3
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1.9k
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Outputting DP4 flag in GATK
variant calling sequencing gatk
updated 7.1 years ago by 5.7k • written 7.1 years ago by ▴ 530
0
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1
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1.6k
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Comment: C: Getting reads that end at a digest site from a sam/bam file
7.1 years ago by Jautis ▴ 530
0
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0
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1.6k
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Comment: C: Getting reads that end at a digest site from a sam/bam file
7.1 years ago by Jautis ▴ 530
0
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7
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1.6k
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Getting reads that end at a digest site from a sam/bam file
bisulfite digest
updated 7.1 years ago by 161k • written 7.1 years ago by ▴ 530
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1
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1.6k
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Comment: C: Getting reads that end at a digest site from a sam/bam file
7.1 years ago by Jautis ▴ 530
0
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1
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1.8k
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Calling allele-specific methylation from bisulfite sequencing reads
bisulfite-sequencing allele-specific sequencing
updated 7.2 years ago by 14k • written 7.2 years ago by ▴ 530
1
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1
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5.8k
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Comment: C: Downsampling bam file to 2x coverage
7.3 years ago by Jautis ▴ 530
0
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1
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3.8k
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Comment: C: Numbers of Samples per Lane in RNAseq
7.3 years ago by Jautis ▴ 530
0
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2
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5.8k
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Comment: C: Downsampling bam file to 2x coverage
7.3 years ago by Jautis ▴ 530
0
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1
reply
3.8k
views
Comment: C: Numbers of Samples per Lane in RNAseq
7.3 years ago by Jautis ▴ 530
5
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7
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5.8k
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Downsampling bam file to 2x coverage
bam sequencing high-throughput
7.3 years ago by Jautis ▴ 530
0
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0
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2.5k
views
Comment: C: Batch effect of RRBS data (Methylation): Elimination and Pipleline
7.5 years ago by Jautis ▴ 530
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