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71
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15
replies
48k
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10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.0 years ago by ▴ 420
2
votes
6
replies
3.0k
views
PRSice: how to obtain exact list of SNPs used for PRSice.best
PRS PRSice PLINK
updated 15 months ago by ★ 4.7k • written 3.5 years ago by ▴ 420
0
votes
0
replies
1.8k
views
IMPUTE2: change names of specific SNPs
impute2 SNPs names
updated 3.4 years ago by 20 • written 6.6 years ago by ▴ 420
0
votes
1
reply
1.3k
views
IMPUTE2: how to dynamically obtain chunks for each chromosome
IMPUTE2 chunks
updated 3.8 years ago by ▴ 30 • written 3.8 years ago by ▴ 420
1
vote
1
reply
2.4k
views
R: How to test for trend of risk scores
R trend test risk scores
updated 3.8 years ago by 20 • written 6.6 years ago by ▴ 420
0
votes
0
replies
667
views
How to do pathway analysis on kinome Drosophila dataset
pathway-analysis GO kinome statistical-power
updated 3.9 years ago by 20 • written 4.1 years ago by ▴ 420
3
votes
2
replies
1.7k
views
variableStep vs fixedStep for range formats
ucsc formats bigwig bedgraph range
updated 4.2 years ago by 20 • written 5.6 years ago by ▴ 420
0
votes
0
replies
806
views
Resources recommendations for cloud computing (AWS) beginners
cloud aws hpc
updated 10 months ago by 43k • written 4.2 years ago by ▴ 420
0
votes
0
replies
593
views
Software design book/resource recommendation for bioinformaticians
python RNA-Seq software-design best-practise
4.5 years ago by m98 ▴ 420
5
votes
3
replies
11k
views
Installing MultiQC on Ubuntu
ngs fastqc multiqc
updated 4.5 years ago by ★ 1.4k • written 5.8 years ago by ▴ 420
5
votes
3
replies
2.2k
views
R: How to save Mart object (BiomaRt package)
R BiomaRt RNA-Seq
updated 4.8 years ago by ★ 2.0k • written 4.8 years ago by ▴ 420
0
votes
0
replies
1.9k
views
Comment: C: Is DAVID an over-representation (ORA) tool for pathway analysis
5.1 years ago by m98 ▴ 420
1
vote
2
replies
1.9k
views
Is DAVID an over-representation (ORA) tool for pathway analysis
DAVID pathway-analysis
updated 5.1 years ago by 35k • written 5.1 years ago by ▴ 420
3
votes
0
replies
9.0k
views
edgeR: how to make contrasts with makeContrasts
ngs edgeR makeContrasts glm dge
5.4 years ago by m98 ▴ 420
1
vote
2
replies
2.4k
views
Reformating bedGraph files in shell script
bedGraph bigWig ucsc chr awk
updated 5.5 years ago by 20 • written 5.6 years ago by ▴ 420
1
vote
0
replies
1.7k
views
UCSC hub: autoscale option for multiwig track
ucsc multiWig track autoscale
5.6 years ago by m98 ▴ 420
0
votes
0
replies
1.7k
views
Comment: C: variableStep vs fixedStep for range formats
5.6 years ago by m98 ▴ 420
0
votes
0
replies
2.4k
views
Comment: C: Reformating bedGraph files in shell script
5.6 years ago by m98 ▴ 420
0
votes
1
reply
3.4k
views
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
5.6 years ago by m98 ▴ 420
0
votes
1
reply
3.4k
views
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
5.6 years ago by m98 ▴ 420
0
votes
1
reply
3.4k
views
Comment: C: Output bedGraph from genomeCoverageBed is missing "chr"
5.6 years ago by m98 ▴ 420
5
votes
8
replies
3.4k
views
Output bedGraph from genomeCoverageBed is missing "chr"
RNA-Seq ucsc genomeCoverageBed bedGraph bigWig
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 420
0
votes
0
replies
13k
views
Comment: C: How to get raw Github URL for a large file
5.6 years ago by m98 ▴ 420
5
votes
3
replies
13k
views
How to get raw Github URL for a large file
ucsc url github
updated 5.6 years ago by ★ 16k • written 5.6 years ago by ▴ 420
25
votes
10
replies
2.9k
views
10 follow
Any suggestions for basic intro to submitting jobs to an HPC cluster?
ngs hpc
updated 11 months ago by 43k • written 5.6 years ago by ▴ 420
0
votes
0
replies
7.4k
views
Comment: C: Understanding subsampling with Samtools
5.7 years ago by m98 ▴ 420
4
votes
5
replies
7.4k
views
Understanding subsampling with Samtools
RNA-Seq subsampling samtools seed reads
updated 2.7 years ago by ▴ 850 • written 5.7 years ago by ▴ 420
8
votes
3
replies
2.7k
views
Normalising RNA-seq samples from bam files for UCSC Genome browser visualization
RNA-Seq ucsc bam bigwig
updated 5.7 years ago by 6.0k • written 5.7 years ago by ▴ 420
13
votes
8
replies
1.7k
views
Comparing reads of multiple BAM files (using getopts for parsing)
bam samtools seqtl getopts
updated 5.7 years ago by 21k • written 5.7 years ago by ▴ 420
0
votes
1
reply
4.8k
views
Comment: C: Different bigwig file sizes between BedgraphToBigwig and bamCoverage
5.7 years ago by m98 ▴ 420
0
votes
1
reply
4.8k
views
Comment: C: Different bigwig file sizes between BedgraphToBigwig and bamCoverage
5.7 years ago by m98 ▴ 420
8
votes
5
replies
4.8k
views
Different bigwig file sizes between BedgraphToBigwig and bamCoverage
ucsc bigwig BedgraphToBigWig bamCoverage deeptools
5.7 years ago by m98 ▴ 420
0
votes
1
reply
3.9k
views
Comment: C: Bam to RPM Bedgraph Conversion
5.7 years ago by m98 ▴ 420
0
votes
1
reply
3.9k
views
Comment: C: Bam to RPM Bedgraph Conversion
5.7 years ago by m98 ▴ 420
0
votes
1
reply
3.9k
views
Comment: C: Bam to RPM Bedgraph Conversion
5.7 years ago by m98 ▴ 420
0
votes
1
reply
1.5k
views
Comment: C: Hosting location for UCSC data hub: cluster v server
5.7 years ago by m98 ▴ 420
0
votes
2
replies
1.5k
views
Comment: C: Hosting location for UCSC data hub: cluster v server
5.7 years ago by m98 ▴ 420
3
votes
6
replies
1.5k
views
Hosting location for UCSC data hub: cluster v server
UCSC data-hub tracks cluster
updated 5.7 years ago by 35k • written 5.7 years ago by ▴ 420
4
votes
13
replies
8.0k
views
Trim_galore on multiple fast.qz files: syntax problem
nsg trim_galore gnu parallel
5.8 years ago by m98 ▴ 420
0
votes
1
reply
8.0k
views
Comment: C: Trim_galore on multiple fast.qz files: syntax problem
5.8 years ago by m98 ▴ 420
0
votes
1
reply
8.0k
views
Comment: C: Trim_galore on multiple fast.qz files: syntax problem
5.8 years ago by m98 ▴ 420
0
votes
0
replies
8.0k
views
Comment: C: Trim_galore on multiple fast.qz files: syntax problem
5.8 years ago by m98 ▴ 420
0
votes
1
reply
8.0k
views
Comment: C: Trim_galore on multiple fast.qz files: syntax problem
5.8 years ago by m98 ▴ 420
11
votes
5
replies
28k
views
FastQC with multiple FASTQ files
ngs fastqc multiple
updated 7 months ago by 43k • written 5.8 years ago by ▴ 420
2
votes
1
reply
1.3k
views
Relationship between sequencing lane and ngs dataset
ngs lane flow-cell
updated 5.8 years ago by 141k • written 5.8 years ago by ▴ 420
16
votes
4
replies
8.9k
views
NGS analysis: how to handle paired-end reads
ngs paired-end reads analysis pipeline
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by ▴ 420
1
vote
0
replies
48k
views
Comment: C: Definition of minor and major allele and connection with risk, effect, wildtype
6.0 years ago by m98 ▴ 420
0
votes
1
reply
48k
views
Comment: C: Definition of minor and major allele and connection with risk, effect, wildtype
6.0 years ago by m98 ▴ 420
0
votes
1
reply
1.9k
views
Obtaining hazard ratio from beta and chi-square values
probabel cox_regression hazard_ratio
updated 6.4 years ago by 87k • written 6.4 years ago by ▴ 420
0
votes
0
replies
1.5k
views
Problem imputing (large) file into GenABEL
GenABEL IMPUTE2 impute2databel
6.5 years ago by m98 ▴ 420
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