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8
votes
5
replies
3.6k
views
Quickly get allele frequencies from Gnomad
gnomad allele freq ngs
updated 18 months ago by ▴ 50 • written 3.7 years ago by ▴ 170
1
vote
2
replies
1.0k
views
get rsID or positions from variant name/gene info
clinvar dbSNP rsID variants
3.5 years ago by Floydian_slip ▴ 170
0
votes
0
replies
623
views
get cDNA start and end for exons in a list of genes
next-gen sequence gene
updated 11 months ago by 43k • written 3.5 years ago by ▴ 170
0
votes
6
replies
2.6k
views
average depth of each region in a BED file calculated from a BAM file
BED BAM coverage NGS
3.7 years ago by Floydian_slip ▴ 170
0
votes
3
replies
745
views
Is reusing a subset of features in another layer of classification wrong or over-fitting?
machine learning overfitting overtraining
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 170
0
votes
0
replies
1.6k
views
Confusing Picard HsMetrics ON_BAIT_VS_SELECTED for near=250 and near=0
sequencing next-gen picard HsMetrics
4.2 years ago by Floydian_slip ▴ 170
0
votes
4
replies
1.1k
views
Calculate the area covered more than a certain depth
next-gen sequencing bam coverage
updated 4.5 years ago by ▴ 580 • written 4.5 years ago by ▴ 170
1
vote
3
replies
1.9k
views
Dragen alignment failing/terminating
dragen alignment
4.6 years ago by Floydian_slip ▴ 170
5
votes
3
replies
1.6k
views
List of conditions a set of genes are associated with in OMIM
OMIM
updated 4.6 years ago by ▴ 600 • written 4.6 years ago by ▴ 170
0
votes
4
replies
931
views
Bed file of union of all transcripts for a set of genes
transcripts gene exons
updated 4.6 years ago by ★ 3.8k • written 4.6 years ago by ▴ 170
3
votes
3
replies
2.8k
views
Popular CNV detection tools
CNV NGS
updated 4.6 years ago by 87k • written 4.6 years ago by ▴ 170
2
votes
5
replies
2.2k
views
Difference between variant calling and genotyping
variant calling genotyping
updated 4.6 years ago by 8.2k • written 4.6 years ago by ▴ 170
0
votes
0
replies
2.5k
views
Using GIAB exome data to test targetome variant-calling pipeline
whole-exome targetome variant-calling GIAB
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 170
2
votes
1
reply
2.0k
views
Mapability index (track) from UCSC
UCSC mapability
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 170
4
votes
7
replies
5.0k
views
picard tools HsMetrics not using duplicate reads to calculate coverage
picard duplicates HsMetrics
updated 6.0 years ago by 20 • written 8.0 years ago by ▴ 170
1
vote
3
replies
1.7k
views
GATK HC not calling variants at the edges after clipping probes
GATK sequencing
6.3 years ago by Floydian_slip ▴ 170
0
votes
12
replies
1.9k
views
Remove hundreds of probes
probes trimming
updated 6.5 years ago by ★ 2.5k • written 6.5 years ago by ▴ 170
0
votes
18
replies
5.6k
views
cuffmerge does not give merged.gtf
RNA-Seq Assembly sequencing alignment
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 170
0
votes
5
replies
6.7k
views
Picard MarkDuplicates error: Value was put into PairInfoMap more than once
Bedtools MarkDuplicates Samtools picard
updated 21 months ago by 43k • written 8.2 years ago by ▴ 170
7
votes
8
replies
4.1k
views
Similarity between two sets of paired-end fastq files
fastq paired-end RNA-Seq
updated 8.1 years ago by ▴ 480 • written 8.1 years ago by ▴ 170
5
votes
6
replies
3.2k
views
QC tool for targeted gene panel (like FastQC for WGS)
QC targeted-gene panel
updated 8.1 years ago by 8.2k • written 8.1 years ago by ▴ 170
1
vote
3
replies
2.8k
views
extracting genotypes from a multi-sample VCF that have certain variants
vcf genotypes
8.1 years ago by Floydian_slip ▴ 170
0
votes
0
replies
2.1k
views
Mapability index from UCSC
mapability UCSC
8.2 years ago by Floydian_slip ▴ 170
6
votes
10
replies
8.4k
views
demultiplexing tool for dual-indexed paired-end illumina libraries
demultiplexing
updated 8.2 years ago by ★ 2.9k • written 8.2 years ago by ▴ 170
4
votes
3
replies
4.7k
views
demultiplexing Illumina output with fastq_multx
demultiplexing
8.2 years ago by Floydian_slip ▴ 170
0
votes
3
replies
1.7k
views
high depth Illumina samples from 1000 Genomes
1000 Genomes
updated 8.2 years ago by ★ 2.2k • written 8.2 years ago by ▴ 170
2
votes
4
replies
9.2k
views
difference between BWA mem, sampe and bwasw
BWA paired-end
updated 21 months ago by 43k • written 8.2 years ago by ▴ 170
1
vote
1
reply
3.9k
views
importance of known sites/resources in GATK pipeline
Quality-Score-relcalibration GATK
updated 24 months ago by 43k • written 9.2 years ago by ▴ 170
0
votes
4
replies
3.4k
views
EdgeR: different values in expression and differential expression tables
EdgeR differential-expression
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 170
2
votes
2
replies
5.2k
views
GATK VariantRecalibrator error: Values for DP annotation not detected for ANY training variant
gatk variantRecalibrator
updated 24 months ago by 43k • written 9.2 years ago by ▴ 170
1
vote
4
replies
3.9k
views
Known SNPs for rice for Base recalibration using GATK
sequencing SNP
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 170
4
votes
5
replies
3.0k
views
Individual or population level variant calling?
SNP population gatk variant-calling
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 170
1
vote
3
replies
3.3k
views
number of .bam reads mapping to genes in gff format
mapping bams gff
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 170
33 results • Page 1 of 1
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