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32
votes
10
replies
19k
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8 follow
How to efficiently remove a list of reads from BAM file?
RNA-Seq BAM samtools Sam
updated 3.3 years ago by 3.1k • written 9.8 years ago by ▴ 540
9
votes
4
replies
9.9k
views
Genetic Map file format: how to understand the combined_rate column and the genetic_map column ?
genetic map centimorgan
updated 5.1 years ago by • 0 • written 9.0 years ago by ▴ 540
0
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0
replies
2.0k
views
Comment: C: Plink with hwe option does not work
5.5 years ago by Tao ▴ 540
0
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1
reply
2.0k
views
Answer: A: Plink with hwe option does not work
5.5 years ago by Tao ▴ 540
0
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1
reply
3.2k
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Answer: A: color gradient for heatmap2
5.5 years ago by Tao ▴ 540
0
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0
replies
2.9k
views
Comment: C: How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
5.5 years ago by Tao ▴ 540
0
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0
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2.9k
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Comment: C: How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
5.5 years ago by Tao ▴ 540
0
votes
4
replies
2.9k
views
How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
snp reference allele ref allele
5.5 years ago by Tao ▴ 540
4
votes
0
replies
19k
views
Comment: C: How to efficiently remove a list of reads from BAM file?
updated 5.9 years ago by 45k • written 9.8 years ago by ▴ 540
0
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0
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19k
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Comment: C: How to efficiently remove a list of reads from BAM file?
updated 5.9 years ago by 45k • written 9.8 years ago by ▴ 540
0
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0
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2.0k
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Comment: C: Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
5.9 years ago by Tao ▴ 540
0
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1
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2.0k
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Comment: C: Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
5.9 years ago by Tao ▴ 540
2
votes
4
replies
2.0k
views
Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
plink --ld LD
updated 5.9 years ago by 11k • written 5.9 years ago by ▴ 540
0
votes
0
replies
4.7k
views
Comment: C: Recoding bim to vcf file with forcing allele-A1
6.4 years ago by Tao ▴ 540
0
votes
0
replies
1.4k
views
How to do Meta-analysis of statistics from T-tests and Wilcoxon rank sum tests?
meta analysis t test wilcoxon rank sum
6.5 years ago by Tao ▴ 540
2
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1
reply
3.3k
views
Answer: A: "hrc-1000g-check-bim.py" Unable to open specified bim file
6.5 years ago by Tao ▴ 540
0
votes
0
replies
1.6k
views
How to define the LD interval where a SNP locates?
LD genetics plink
6.9 years ago by Tao ▴ 540
8
votes
3
replies
2.8k
views
How to get gene full description with Ensembl IDs?
gene annotation Ensembl
updated 7.1 years ago by 12k • written 8.7 years ago by ▴ 540
0
votes
0
replies
2.0k
views
Answer: A: How to match alleles for a pair of SNPs using PLINK?
7.4 years ago by Tao ▴ 540
0
votes
1
reply
2.0k
views
How to match alleles for a pair of SNPs using PLINK?
LD Allele matching Plink
7.4 years ago by Tao ▴ 540
1
vote
1
reply
15k
views
Comment: C: Calculating TPM Values
7.6 years ago by Tao ▴ 540
5
votes
1
reply
15k
views
Answer: A: Calculating TPM Values
7.6 years ago by Tao ▴ 540
1
vote
0
replies
74k
views
Comment: Comment: RNA-seq: Explain STAR quantMode geneCounts values
7.6 years ago by Tao ▴ 540
1
vote
0
replies
14k
views
Comment: C: WGCNA signed vs unsigned network
7.9 years ago by Tao ▴ 540
6
votes
1
reply
14k
views
Answer: A: WGCNA signed vs unsigned network
7.9 years ago by Tao ▴ 540
0
votes
0
replies
21k
views
Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
7.9 years ago by Tao ▴ 540
4
votes
0
replies
24k
views
Answer: A: What exactly is sequencing depth in RNAseq?
8.0 years ago by Tao ▴ 540
0
votes
1
reply
5.1k
views
Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
8.0 years ago by Tao ▴ 540
0
votes
1
reply
5.1k
views
Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
8.0 years ago by Tao ▴ 540
0
votes
0
replies
4.0k
views
Comment: C: Imputation on two genotyping datasets: should I do imputation separately? or mer
8.0 years ago by Tao ▴ 540
0
votes
1
reply
5.1k
views
Comment: C: Does it make sense to perform Genotype Imputation using variants called from WES
8.0 years ago by Tao ▴ 540
4
votes
7
replies
5.1k
views
Does it make sense to perform Genotype Imputation using variants called from WES?
genotype imputation Whole Exon Sequencing variants
8.0 years ago by Tao ▴ 540
1
vote
5
replies
5.4k
views
In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
GWAS
updated 8.5 years ago by 8.9k • written 8.5 years ago by ▴ 540
0
votes
1
reply
5.4k
views
Comment: A: In GWAS Studies, how to understand "97 SNPs explain 2.7% of BMI"?
8.5 years ago by Tao ▴ 540
1
vote
1
reply
16k
views
Comment: C: How to remove a list of reads from fastq file?
8.5 years ago by Tao ▴ 540
1
vote
0
replies
4.4k
views
Answer: A: How to access VCF files for Genotype Tissue Expression (GTEx) data
8.7 years ago by Tao ▴ 540
0
votes
0
replies
21k
views
Answer: A: Filtering Imputation output: how to filter on a VCF INFO field
8.9 years ago by Tao ▴ 540
0
votes
0
replies
21k
views
Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
8.9 years ago by Tao ▴ 540
1
vote
1
reply
2.6k
views
Answer: A: paste columns into one line in command line
9.0 years ago by Tao ▴ 540
1
vote
1
reply
4.0k
views
Imputation on two genotyping datasets: should I do imputation separately? or merge the two datasets first?
imputation genotyping eQTL SNPs
9.0 years ago by Tao ▴ 540
1
vote
0
replies
1.9k
views
Can I do eqtl mapping combining RNA-seq and Microarray data?
eqtl RNA-Seq microarray
9.2 years ago by Tao ▴ 540
0
votes
0
replies
7.0k
views
Answer: A: Paired-end RNA Seq data: How to deal with unpaired data after trimmomatic
9.3 years ago by Tao ▴ 540
0
votes
0
replies
16k
views
Comment: C: How to remove a list of reads from fastq file?
9.3 years ago by Tao ▴ 540
10
votes
9
replies
16k
views
6 follow
How to remove a list of reads from fastq file?
fastq shell bash script
updated 3.0 years ago by • 0 • written 9.3 years ago by ▴ 540
0
votes
1
reply
16k
views
Answer: A: How to remove a list of reads from fastq file?
9.3 years ago by Tao ▴ 540
0
votes
0
replies
16k
views
Comment: C: How to remove a list of reads from fastq file?
9.3 years ago by Tao ▴ 540
0
votes
0
replies
4.9k
views
Comment: C: Should I use reads with good quality but failed-vendor flag?
9.4 years ago by Tao ▴ 540
0
votes
1
reply
4.9k
views
Comment: C: Should I use reads with good quality but failed-vendor flag?
9.4 years ago by Tao ▴ 540
4
votes
7
replies
4.9k
views
Should I use reads with good quality but failed-vendor flag?
sam vendor failed sam flag chastity score
updated 9.4 years ago by ★ 1.2k • written 9.4 years ago by ▴ 540
0
votes
0
replies
4.9k
views
Comment: C: Should I use reads with good quality but failed-vendor flag?
9.4 years ago by Tao ▴ 540
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