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22
votes
10
replies
10k
views
9 follow
fastq compression tools of choice
fastq compression
updated 16 months ago by • 0 • written 9.8 years ago by ▴ 600
1
vote
2
replies
2.8k
views
annotate VCF file with LRG ?
LRG vcf annotation
updated 3.6 years ago by 45k • written 10.9 years ago by ▴ 600
6
votes
8
replies
3.9k
views
IGV over SSH?
IGV SSH remote
updated 3.9 years ago by 45k • written 4.5 years ago by ▴ 600
0
votes
0
replies
1.5k
views
Answer: A: SnpSift set intersection with EFF annotations
4.5 years ago by Richard ▴ 600
0
votes
1
reply
1.5k
views
SnpSift set intersection with EFF annotations
snpsift variant annotation parsing
4.5 years ago by Richard ▴ 600
0
votes
1
reply
960
views
classify contaminants in bisulfite treated whole genome data
wgbs
updated 4.7 years ago by 9.0k • written 4.7 years ago by ▴ 600
0
votes
0
replies
1.3k
views
Comment: C: Calling CNVs using a single tumor sample
4.8 years ago by Richard ▴ 600
0
votes
0
replies
1.3k
views
Answer: A: Manually Search Sam/Bam File
4.8 years ago by Richard ▴ 600
0
votes
3
replies
1.2k
views
creating container - should it contain a workflow manager?
singularity snakemake nextflow
updated 5.1 years ago by 23k • written 5.1 years ago by ▴ 600
3
votes
0
replies
40k
views
Answer: A: Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
updated 5.5 years ago by 45k • written 11.1 years ago by ▴ 600
1
vote
0
replies
2.9k
views
Answer: C: Affy 500K positions in hg38
updated 5.5 years ago by 45k • written 9.5 years ago by ▴ 600
0
votes
2
replies
1.6k
views
matched designed sequence in nanopore reads
sequence alignment
updated 5.5 years ago by ▴ 120 • written 5.5 years ago by ▴ 600
1
vote
2
replies
2.8k
views
multiqc change sample names
multiqc
5.9 years ago by Richard ▴ 600
1
vote
0
replies
2.8k
views
Answer: A: multiqc change sample names
5.9 years ago by Richard ▴ 600
0
votes
0
replies
2.8k
views
Comment: C: multiqc change sample names
5.9 years ago by Richard ▴ 600
1
vote
4
replies
2.0k
views
UMI with MACS
UMI MACS ChIP-Seq
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 600
0
votes
0
replies
2.0k
views
Comment: C: UMI with MACS
6.1 years ago by Richard ▴ 600
0
votes
1
reply
2.0k
views
Comment: C: UMI with MACS
6.1 years ago by Richard ▴ 600
0
votes
1
reply
4.2k
views
Comment: C: beginner snakemake scatter gather help
6.3 years ago by Richard ▴ 600
0
votes
1
reply
4.2k
views
Comment: C: beginner snakemake scatter gather help
6.3 years ago by Richard ▴ 600
4
votes
8
replies
4.2k
views
beginner snakemake scatter gather help
snakemake
6.3 years ago by Richard ▴ 600
0
votes
1
reply
4.2k
views
Comment: A: beginner snakemake scatter gather help
6.3 years ago by Richard ▴ 600
2
votes
1
reply
3.7k
views
does bwa mem use base qualities?
bwa
updated 2.9 years ago by 45k • written 9.4 years ago by ▴ 600
0
votes
0
replies
1.1k
views
MD tags - important for analysis tools?
BAM MD
6.4 years ago by Richard ▴ 600
3
votes
3
replies
3.0k
views
miRNA with UMI - any papers showing this improves accuracy?
miRNA UMI
updated 6.4 years ago by ▴ 50 • written 7.0 years ago by ▴ 600
0
votes
0
replies
2.6k
views
Comment: C: how to fix old VCF headers
updated 6.7 years ago by 16k • written 6.7 years ago by ▴ 600
0
votes
1
reply
2.6k
views
how to fix old VCF headers
VCF
6.7 years ago by Richard ▴ 600
2
votes
1
reply
1.1k
views
Human Promethion data available?
sequence
updated 6.7 years ago by 48k • written 6.7 years ago by ▴ 600
0
votes
1
reply
1.1k
views
Germline genome ground truth sets
ground truth
updated 6.8 years ago by 20 • written 6.9 years ago by ▴ 600
0
votes
0
replies
1.4k
views
merge aligned read pairs that overlap - keep the bases that match the reference
paired-end illumina
7.0 years ago by Richard ▴ 600
17
votes
9
replies
9.1k
views
6 follow
compare SV results across samples - Manta, Delly
manta delly wgs illumina
updated 3.8 years ago by • 0 • written 7.1 years ago by ▴ 600
0
votes
1
reply
3.0k
views
Comment: C: merge Bed entries with both ends within maximum distance
7.2 years ago by Richard ▴ 600
0
votes
1
reply
3.0k
views
Comment: C: merge Bed entries with both ends within maximum distance
7.2 years ago by Richard ▴ 600
1
vote
1
reply
3.0k
views
Comment: C: merge Bed entries with both ends within maximum distance
7.2 years ago by Richard ▴ 600
2
votes
12
replies
3.0k
views
merge Bed entries with both ends within maximum distance
next-gen alignment
updated 7.2 years ago by 36k • written 7.2 years ago by ▴ 600
0
votes
0
replies
3.0k
views
Comment: C: merge Bed entries with both ends within maximum distance
7.2 years ago by Richard ▴ 600
0
votes
2
replies
4.4k
views
extract reads from BAM whose fragments overlap a specified region
alignment
updated 7.2 years ago by 166k • written 7.2 years ago by ▴ 600
2
votes
1
reply
1.1k
views
estimate error profile from aligned Illumina reads
illumina error_rate
updated 7.5 years ago by ★ 4.0k • written 7.5 years ago by ▴ 600
0
votes
4
replies
2.9k
views
auto trimming of adapter and 6 base normalizing sequence from miRNA reads
microRNA trimming adapters
updated 2.9 years ago by 45k • written 9.5 years ago by ▴ 600
4
votes
4
replies
2.8k
views
simulating illumina data with spiked variants
simulated-data illumina
updated 3.6 years ago by 45k • written 11.0 years ago by ▴ 600
0
votes
0
replies
2.2k
views
Comment: C: proximal duplicate parameters - HiSeq X
8.3 years ago by Richard ▴ 600
0
votes
2
replies
2.2k
views
proximal duplicate parameters - HiSeq X
duplicates proximal
updated 8.3 years ago by 152k • written 8.3 years ago by ▴ 600
2
votes
3
replies
2.9k
views
Affy 500K positions in hg38
affymetrix hg38
updated 9.5 years ago by 27k • written 9.5 years ago by ▴ 600
0
votes
1
reply
5.0k
views
Comment: C: variant calling on amplicon data
9.8 years ago by Richard ▴ 600
6
votes
7
replies
5.0k
views
variant calling on amplicon data
amplicon variant
updated 2.7 years ago by 45k • written 9.8 years ago by ▴ 600
5
votes
2
replies
6.1k
views
Answer: Answer: Identify somatic mutations in cancer exome without a matched pair.
updated 3.2 years ago by 45k • written 9.8 years ago by ▴ 600
1
vote
1
reply
2.5k
views
tools using CRAM format?
cram
updated 2.7 years ago by 45k • written 9.8 years ago by ▴ 600
0
votes
1
reply
2.7k
views
Comment: C: merging bed coordinates - get depth and information about merged regions
9.8 years ago by Richard ▴ 600
0
votes
1
reply
2.7k
views
Comment: Comment: merging bed coordinates - get depth and information about merged regions
updated 2.7 years ago by 45k • written 9.8 years ago by ▴ 600
2
votes
4
replies
2.7k
views
merging bed coordinates - get depth and information about merged regions
bed bedtools
updated 2.7 years ago by 45k • written 9.8 years ago by ▴ 600
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