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3
votes
1
reply
566
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 1 day ago by ▴ 20 • written 19 months ago by ★ 4.3k
6
votes
2
replies
736
views
samtools index: failed to create index. ([E::hts_idx_push] NO_COOR reads not in a single block )
bam samtools hisat2
updated 3 months ago by ▴ 680 • written 3 months ago by ★ 4.3k
2
votes
4
replies
582
views
How should I run ssgsea analysis ?
functional TPM enrichment gsea ssgsea
updated 4 months ago by 43k • written 4 months ago by ★ 4.3k
3
votes
1
reply
546
views
How will you perform batch correction in DESeq2 when you don't have any group information?
batch-correction DESeq2
updated 5 months ago by 43k • written 5 months ago by ★ 4.3k
6
votes
1
reply
396
views
How to retrieve sample informations from given ID from Sequence Read Archives?
eutils SRA
updated 5 months ago by 43k • written 7 months ago by ★ 4.3k
2
votes
0
replies
285
views
How to perform functional enrichment of Metabolites?
PerformPSEA metaboanalyst GSEA metabolites
8 months ago by DareDevil ★ 4.3k
7
votes
4
replies
823
views
Are there any ways to delete multiple jobs at Ensembl VEP?
api ensembl vep
updated 8 months ago by ★ 2.4k • written 8 months ago by ★ 4.3k
2
votes
1
reply
447
views
What is the possibility of Depth (DP) being higher than the coverage
GATK DP Coverage Depth HaplotypeCaller
updated 10 months ago by 11k • written 10 months ago by ★ 4.3k
11
votes
3
replies
942
views
How to deal with the probe id mapping to multiple gene ids?
match microarray affymetrix probe gene
12 months ago by DareDevil ★ 4.3k
6
votes
3
replies
747
views
Informations for gene summary are missing in eutils api of NCBI?
NCBI esummary eutils Gene
updated 13 months ago by ▴ 720 • written 13 months ago by ★ 4.3k
5
votes
1
reply
515
views
How do I retrieve withdrawn or replaced gene id for homosapiens from ncbi gene ?
NCBI Eutils
updated 13 months ago by 43k • written 13 months ago by ★ 4.3k
4
votes
0
replies
376
views
How to identify the batch informations from the sample ID?
batch-correction TCGAbatch DESeq2 TCGA
updated 14 months ago by 43k • written 14 months ago by ★ 4.3k
3
votes
2
replies
1.1k
views
A USER ERROR has occurred: Positive training model failed to converge.
gatk vcf max-gaussians
updated 20 months ago by • 0 • written 3.2 years ago by ★ 4.3k
22
votes
2
replies
1.5k
views
How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
VQSR GATK VariantRecalibrator
2.1 years ago by DareDevil ★ 4.3k
2
votes
0
replies
444
views
How is the pvalue in cibersort calculated?
pvalue cibersort
2.3 years ago by DareDevil ★ 4.3k
3
votes
1
reply
799
views
How to perform differential expression analysis of metabric data obtained from METABRIC?
DEseq2 cbioportal EdgeR limma
updated 2.8 years ago by ★ 1.6k • written 2.8 years ago by ★ 4.3k
2
votes
2
replies
719
views
How do I call compound hetrozygosity from multiple trios cohort?
ped gatk trio heterozygosity compound vcf
2.8 years ago by DareDevil ★ 4.3k
1
vote
0
replies
613
views
How to filter the germline INDELS?
INDELS GATK VCF
2.9 years ago by DareDevil ★ 4.3k
12
votes
4
replies
4.1k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 19 months ago by ▴ 160 • written 3.0 years ago by ★ 4.3k
3
votes
2
replies
963
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 3.0 years ago by 81k • written 3.0 years ago by ★ 4.3k
2
votes
0
replies
739
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
3.0 years ago by DareDevil ★ 4.3k
5
votes
2
replies
1.7k
views
Infering strand specificity of bam files using rseqc?
RSeQC bam featureCounts
updated 3.1 years ago by 100k • written 3.1 years ago by ★ 4.3k
4
votes
2
replies
2.2k
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable vcf gatk
3.1 years ago by DareDevil ★ 4.3k
3
votes
1
reply
863
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
3.1 years ago by DareDevil ★ 4.3k
7
votes
7
replies
1.7k
views
How to extract postions from gnomad using tabix?
tabix gnomad vcf
updated 3.1 years ago by 161k • written 3.1 years ago by ★ 4.3k
5
votes
5
replies
4.1k
views
How to convert gvcf file to normal vcf file ?
vcf gatk gvcf
11 months ago by DareDevil ★ 4.3k
2
votes
0
replies
677
views
Is it possible to apply limma on metabric data?
limma metabric mRNA DEG
3.1 years ago by DareDevil ★ 4.3k
2
votes
4
replies
2.5k
views
CIBERSORT: Errors were encountered in input files, run aborted:
deconvolution cibersort
updated 13 months ago by 43k • written 3.2 years ago by ★ 4.3k
0
votes
0
replies
602
views
What is the cut off used in TCGA vcf files for allelic frequency for calling it as somatic?
tcga vcf
3.2 years ago by DareDevil ★ 4.3k
6
votes
4
replies
4.1k
views
Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?
nanostring deseq2 limma
updated 13 months ago by 43k • written 3.2 years ago by ★ 4.3k
4
votes
1
reply
1.2k
views
Are there any repository for panel of normal for running Mutect2?
Mutect2 PON panel of normal gatk
3.2 years ago by DareDevil ★ 4.3k
2
votes
2
replies
679
views
What test can be conducted to check ratio between the groups are significant ?
pvalue statistical test p-value cibersort
3.2 years ago by DareDevil ★ 4.3k
6
votes
6
replies
1.1k
views
Agilent microarray data analysis end in no significant genes ?
microarray r limma
updated 3.2 years ago by 87k • written 3.2 years ago by ★ 4.3k
0
votes
0
replies
618
views
How to perform relatedness across multiple trio cohort ?
trio vcftools relatedness
3.2 years ago by DareDevil ★ 4.3k
16
votes
15
replies
3.0k
views
Is it possible to run haplotypecaller in gnu parallel ?
gnu parallel HaplotypeCaller parallel gatk
3.2 years ago by DareDevil ★ 4.3k
3
votes
6
replies
988
views
How is allelle frequency calculated ?
vcf allelle frequency exome
updated 3.2 years ago by 161k • written 3.2 years ago by ★ 4.3k
10
votes
1
reply
810
views
Calling triovariants using varscan from a compressed mileup file ?
varscan samtools trio mpileup pipe
updated 3.2 years ago by ▴ 680 • written 3.3 years ago by ★ 4.3k
19
votes
5
replies
2.1k
views
Qualimap: java.lang.RuntimeException: The raw data doesn't exist for sample ?
qualimap bamqc multi-bamqc
3.2 years ago by DareDevil ★ 4.3k
8
votes
1
reply
1.2k
views
CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
CalculateGenotypePosteriors gatk trio ped
3.3 years ago by DareDevil ★ 4.3k
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan samtools pipe
3.3 years ago by DareDevil ★ 4.3k
10
votes
4
replies
1.8k
views
Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
GenomicsDBImport GATK trio cohort
3.3 years ago by DareDevil ★ 4.3k
2
votes
4
replies
917
views
How to call denovo variants from multiple trios cohort?
trio denovo gatk germline
updated 3.3 years ago by 161k • written 3.3 years ago by ★ 4.3k
4
votes
0
replies
785
views
How to filter miRNAs from `NanoString nCounter` assay?
NanoString mRNA miRNA nCounter filter
3.3 years ago by DareDevil ★ 4.3k
4
votes
9
replies
1.1k
views
Issues with adapter trimming when there are no adapters?
fastqc cutadapt adapters illumina trimgalore
3.4 years ago by DareDevil ★ 4.3k
16
votes
15
replies
2.8k
views
How to call denovo and rare variants from a trios cohort?
gatk gvcf trio denovo variants
updated 3.4 years ago by 22k • written 3.4 years ago by ★ 4.3k
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