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1.1k
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Convert VCF + LDhelmet Recombination Rates to EIGENSTRAT format
vcf linkage SNP genome
3.6 years ago by Jautis ▴ 510
0
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0
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934
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find position of snps in cM, given recombination map from ldhelmet
recombination genome physical position
3.6 years ago by Jautis ▴ 510
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0
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1.8k
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Comment: C: sed (or similar) command to remove part of the FORMAT from a vcf file?
3.6 years ago by Jautis ▴ 510
2
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2
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1.8k
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sed (or similar) command to remove part of the FORMAT from a vcf file?
vcf sed processing
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 510
0
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1
reply
13k
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Comment: C: How to combine chromosome vcf files
3.6 years ago by Jautis ▴ 510
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0
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2.5k
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Comment: C: Phylogenetic distance betwee species
updated 3.8 years ago by 40k • written 7.8 years ago by ▴ 510
2
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0
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4.4k
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Comment: C: Good Bioinformatics research papers
updated 3.8 years ago by 40k • written 7.9 years ago by ▴ 510
0
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1
reply
3.3k
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Comment: C: Taking genotypes out of a vcf file
updated 3.9 years ago by 40k • written 8.2 years ago by ▴ 510
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0
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12k
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Comment: C: Calculating the bisulfite conversion rate
updated 3.9 years ago by 40k • written 8.2 years ago by ▴ 510
4
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2
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12k
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Answer: A: Calculating the bisulfite conversion rate
updated 3.9 years ago by 40k • written 8.2 years ago by ▴ 510
0
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0
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1.6k
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Comment: C: vcftools minDP filter not working for samtools genotype calling output
4.0 years ago by Jautis ▴ 510
1
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2
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1.6k
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vcftools minDP filter not working for samtools genotype calling output
genotype filtering SNP SNP-calling
4.0 years ago by Jautis ▴ 510
0
votes
1
reply
841
views
Efficiently run blat for long sequences
blat alignment sequence assembly
updated 4.0 years ago by ★ 2.5k • written 4.1 years ago by ▴ 510
1
vote
1
reply
1.3k
views
Annotate CpG Islands for a new genome
CpG assembly annotation
updated 4.5 years ago by ★ 3.6k • written 4.5 years ago by ▴ 510
1
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8
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2.2k
views
Error in transferring annotations to a new assembly using RATT
alignment annotation software error Assembly
updated 4.6 years ago by 34k • written 4.7 years ago by ▴ 510
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2
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2.2k
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Comment: C: Error in transferring annotations to a new assembly using RATT
4.7 years ago by Jautis ▴ 510
0
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2
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2.2k
views
Comment: C: Error in transferring annotations to a new assembly using RATT
4.7 years ago by Jautis ▴ 510
2
votes
1
reply
2.4k
views
Create a pseudo-haploid fasta file based genotype calls for an individual (vcf file)
vcf sequence assembly SNP
updated 4.9 years ago by ★ 1.6k • written 4.9 years ago by ▴ 510
0
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0
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982
views
Find SNPs which disrupt CpG sites
vcf genome variants
4.9 years ago by Jautis ▴ 510
0
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0
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1.4k
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Determine the derived allele
alignment
5.1 years ago by Jautis ▴ 510
0
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0
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2.6k
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Comment: C: GOseq with non-supported organism
5.2 years ago by Jautis ▴ 510
1
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2
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2.6k
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GOseq with non-supported organism
GO GOseq R
5.2 years ago by Jautis ▴ 510
0
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1
reply
1.3k
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Comment: C: Find chromosomal location of a scaffold
5.2 years ago by Jautis ▴ 510
0
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1
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1.3k
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Comment: C: Find chromosomal location of a scaffold
5.2 years ago by Jautis ▴ 510
1
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5
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1.3k
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Find chromosomal location of a scaffold
genome mapping
updated 5.2 years ago by 34k • written 5.2 years ago by ▴ 510
0
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1
reply
3.5k
views
Comment: C: Convert an altered sam file into a bam file
5.8 years ago by Jautis ▴ 510
3
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4
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3.5k
views
Convert an altered sam file into a bam file
sam bam sequencing
5.8 years ago by Jautis ▴ 510
0
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0
replies
1.7k
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BSMap to Bismark bam file formats
next-gen sequencing bam bisulfite
5.8 years ago by Jautis ▴ 510
0
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0
replies
1.1k
views
Comment: C: Genotype calls for a list of variable sites
5.9 years ago by Jautis ▴ 510
0
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2
replies
1.1k
views
Genotype calls for a list of variable sites
genotype-calling GATK variant-calling
updated 6.0 years ago by 157k • written 6.0 years ago by ▴ 510
1
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0
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6.5k
views
Comment: C: Modifying fasta file based on vcf information
6.3 years ago by Jautis ▴ 510
10
votes
4
replies
5.8k
views
Comparing two phylogenies
covariance phylogeny tree
updated 12 months ago by 40k • written 8.0 years ago by ▴ 510
0
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1
reply
1.7k
views
Comment: C: Outputting DP4 flag in GATK
6.5 years ago by Jautis ▴ 510
2
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3
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1.7k
views
Outputting DP4 flag in GATK
variant calling sequencing gatk
updated 6.5 years ago by 5.7k • written 6.5 years ago by ▴ 510
0
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1
reply
1.5k
views
Comment: C: Getting reads that end at a digest site from a sam/bam file
6.6 years ago by Jautis ▴ 510
0
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0
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1.5k
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Comment: C: Getting reads that end at a digest site from a sam/bam file
6.6 years ago by Jautis ▴ 510
0
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7
replies
1.5k
views
Getting reads that end at a digest site from a sam/bam file
bisulfite digest
updated 6.6 years ago by 157k • written 6.6 years ago by ▴ 510
0
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1
reply
1.5k
views
Comment: C: Getting reads that end at a digest site from a sam/bam file
6.6 years ago by Jautis ▴ 510
0
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1
reply
1.7k
views
Calling allele-specific methylation from bisulfite sequencing reads
bisulfite-sequencing allele-specific sequencing
updated 6.7 years ago by 14k • written 6.7 years ago by ▴ 510
1
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1
reply
5.4k
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Comment: C: Downsampling bam file to 2x coverage
6.7 years ago by Jautis ▴ 510
0
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1
reply
3.6k
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Comment: C: Numbers of Samples per Lane in RNAseq
6.7 years ago by Jautis ▴ 510
0
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2
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5.4k
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Comment: C: Downsampling bam file to 2x coverage
6.7 years ago by Jautis ▴ 510
0
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1
reply
3.6k
views
Comment: C: Numbers of Samples per Lane in RNAseq
6.7 years ago by Jautis ▴ 510
5
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7
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5.4k
views
Downsampling bam file to 2x coverage
bam sequencing high-throughput
6.7 years ago by Jautis ▴ 510
0
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0
replies
2.3k
views
Comment: C: Batch effect of RRBS data (Methylation): Elimination and Pipleline
7.0 years ago by Jautis ▴ 510
0
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1
reply
1.2k
views
high coverage but few genotype calls: possible causes?+
genotype calling sequencing SNP
7.4 years ago by Jautis ▴ 510
3
votes
4
replies
5.3k
views
Compare tree topologies (Newick)
tree phylogeny gene
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 510
0
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1
reply
5.3k
views
Comment: C: Compare tree topologies (Newick)
7.6 years ago by Jautis ▴ 510
0
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1
reply
1.4k
views
Check for Msp1 digestion in sequencing data
RRBS digestion bisulfite-sequencing msp1
updated 14 months ago by 40k • written 7.7 years ago by ▴ 510
0
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0
replies
2.4k
views
Genome sites from BPM file
illumina location bpm
updated 13 months ago by 40k • written 7.8 years ago by ▴ 510
145 results • Page 2 of 3
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