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Comment: Comment: ancestral allele SNP mouse biomart
20 months ago by serpalma.v ▴ 70
3
votes
3
replies
796
views
ancestral allele SNP mouse biomart
biomart ensembl mouse snp
updated 20 months ago by 23k • written 20 months ago by ▴ 70
0
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0
replies
500
views
Evaluating RMSMappingQuality profile to set threshold
SNP snp gatk variant calling filtering
updated 3.0 years ago by 10k • written 3.0 years ago by ▴ 70
8
votes
8
replies
2.5k
views
Only females but still few reads map to Y chromosome
bwa WGS alignment
updated 3.0 years ago by 20 • written 4.6 years ago by ▴ 70
0
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0
replies
810
views
Comment: C: Insert size 350bp vs 400bp, any major downstream difference?
3.1 years ago by serpalma.v ▴ 70
1
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2
replies
810
views
Insert size 350bp vs 400bp, any major downstream difference?
SNP alignment sequencing
3.1 years ago by serpalma.v ▴ 70
0
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0
replies
593
views
how can I extract intervals from bed file spanning a max larger interval in a windowed mode without disrupting intervals?
sequencing bed bedtools bedops
3.2 years ago by serpalma.v ▴ 70
0
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1
reply
877
views
Comment: C: How to extract intervals for regions that are masked?
3.2 years ago by serpalma.v ▴ 70
1
vote
3
replies
877
views
How to extract intervals for regions that are masked?
SNP sequencing assembly
3.2 years ago by serpalma.v ▴ 70
0
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0
replies
1.2k
views
Comment: C: Are there any issues with using sample reads coming from different technologies
3.3 years ago by serpalma.v ▴ 70
1
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7
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1.2k
views
Are there any issues with using sample reads coming from different technologies and having different depths to do joint variant calling (gatk)?
gatk SNP variant calling hiseq novaseq
updated 3.3 years ago by ▴ 410 • written 3.3 years ago by ▴ 70
0
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1
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1.2k
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Comment: C: Are there any issues with using sample reads coming from different technologies
3.3 years ago by serpalma.v ▴ 70
0
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0
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1.7k
views
Comment: C: What test to apply to detect genomic signatures of selection?
updated 3.5 years ago by 39k • written 7.4 years ago by ▴ 70
2
votes
1
reply
2.1k
views
How to replicate vcftool's sliding window SNP density?
SNP sequencing vcftools
updated 3.7 years ago by ★ 2.5k • written 3.7 years ago by ▴ 70
0
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0
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1.6k
views
Comment: C: How does plink calculates linkage disequilibrium (r2) in unphased data?
3.8 years ago by serpalma.v ▴ 70
0
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2
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1.6k
views
How does plink calculates linkage disequilibrium (r2) in unphased data?
plink SNP sequencing
updated 3.8 years ago by 10k • written 3.8 years ago by ▴ 70
0
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1
reply
1.1k
views
Comment: C: Interpretation of full LD between extremely distant SNPs
4.0 years ago by serpalma.v ▴ 70
0
votes
3
replies
1.1k
views
Interpretation of full LD between extremely distant SNPs
linkage disequilibrium SNP
updated 4.1 years ago by 85k • written 4.1 years ago by ▴ 70
1
vote
0
replies
1.8k
views
How to set the size of window for calculating Fst?
SNP Fst window
4.1 years ago by serpalma.v ▴ 70
0
votes
0
replies
820
views
Scanning for selection using rehh2 from mouse WGS VCF
rehh2 sequencing mouse
4.1 years ago by serpalma.v ▴ 70
0
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0
replies
1.8k
views
How to detect outliers from either (a) SNP-Fst or (b) Window-Fst distributions?
Fst vcftools
updated 4.2 years ago by 34k • written 4.2 years ago by ▴ 70
0
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0
replies
1.4k
views
Reference TiTv ratio for mouse WGS?
SNP mouse TiTv Transition Transversion
updated 4.2 years ago by 20 • written 4.4 years ago by ▴ 70
0
votes
1
reply
14k
views
Comment: C: Best tool for variant calling
4.3 years ago by serpalma.v ▴ 70
0
votes
1
reply
14k
views
Comment: C: Best tool for variant calling
4.3 years ago by serpalma.v ▴ 70
0
votes
1
reply
14k
views
Comment: C: Best tool for variant calling
4.3 years ago by serpalma.v ▴ 70
0
votes
0
replies
1.1k
views
Are both samtools mpileup options -m and -F only related to indel detection?
mpileup samtools next-gen alignment SNP
4.3 years ago by serpalma.v ▴ 70
0
votes
0
replies
958
views
Comment: C: How to select SNPs the most conservative way after WGS Variant Calling?
4.3 years ago by serpalma.v ▴ 70
0
votes
2
replies
958
views
How to select SNPs the most conservative way after WGS Variant Calling?
SNP sequencing next-gen
updated 4.3 years ago by 98k • written 4.3 years ago by ▴ 70
0
votes
1
reply
14k
views
Comment: C: Best tool for variant calling
4.3 years ago by serpalma.v ▴ 70
0
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0
replies
3.8k
views
Comment: C: Overrepresented stretches of Gs in NovaSeq library
4.4 years ago by serpalma.v ▴ 70
0
votes
1
reply
11k
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Comment: C: what cause poly-G from NextSeq
4.4 years ago by serpalma.v ▴ 70
0
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2
replies
3.8k
views
Comment: C: Overrepresented stretches of Gs in NovaSeq library
4.4 years ago by serpalma.v ▴ 70
0
votes
4
replies
3.8k
views
Overrepresented stretches of Gs in NovaSeq library
fastqc sequencing DNA
updated 4.4 years ago by ★ 3.8k • written 4.4 years ago by ▴ 70
0
votes
0
replies
1.0k
views
History of the mouse genome
mouse genome sequencing
updated 4.4 years ago by 20 • written 4.5 years ago by ▴ 70
0
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1
reply
3.0k
views
Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
4.5 years ago by serpalma.v ▴ 70
0
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1
reply
3.0k
views
Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
4.5 years ago by serpalma.v ▴ 70
2
votes
5
replies
3.0k
views
bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
bcftools samtools mpileup WGS snp
4.5 years ago by serpalma.v ▴ 70
0
votes
0
replies
2.3k
views
Comment: C: GATK variantFiltration unexpected behaviour?
4.5 years ago by serpalma.v ▴ 70
0
votes
1
reply
2.5k
views
Comment: C: Only females but still few reads map to Y chromosome
4.6 years ago by serpalma.v ▴ 70
0
votes
1
reply
2.5k
views
Comment: C: Only females but still few reads map to Y chromosome
4.6 years ago by serpalma.v ▴ 70
0
votes
0
replies
2.5k
views
Comment: C: Only females but still few reads map to Y chromosome
4.6 years ago by serpalma.v ▴ 70
0
votes
0
replies
1.8k
views
Comment: C: Per base GC content with a shoulder after adapter removal and trimming
4.7 years ago by serpalma.v ▴ 70
0
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1
reply
1.8k
views
Comment: C: Per base GC content with a shoulder after adapter removal and trimming
4.7 years ago by serpalma.v ▴ 70
0
votes
6
replies
1.8k
views
Per base GC content with a shoulder after adapter removal and trimming
fastqc GC content
4.7 years ago by serpalma.v ▴ 70
1
vote
4
replies
2.4k
views
Adding read group to bam files from multiplexed samples
bam picard gatk
updated 4.7 years ago by 20 • written 4.9 years ago by ▴ 70
0
votes
0
replies
1.8k
views
Discrepancy in gene set size between gage() and geneData()
gage pathview kegg pathway analysis
updated 4.7 years ago by 39k • written 7.3 years ago by ▴ 70
0
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0
replies
1.1k
views
Comment: C: what is the conventional apporach to calculate depth of coverage?
4.7 years ago by serpalma.v ▴ 70
1
vote
3
replies
1.1k
views
what is the conventional apporach to calculate depth of coverage?
coverage SNP WGS dnaseq depth
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 70
0
votes
9
replies
1.9k
views
Which indication of a failure can be found in bwa-mem or samtools' output?
bwa samtools
updated 4.8 years ago by 72k • written 4.8 years ago by ▴ 70
0
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1
reply
1.9k
views
Comment: C: Which indication of a failure can be found in bwa-mem or samtools' output?
4.8 years ago by serpalma.v ▴ 70
87 results • Page 1 of 2
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