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1
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0
replies
620
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
amy__
▴ 160 • written 3.0 years ago by
DareDevil
★ 4.3k
3
votes
2
replies
970
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl
VEP
VCF
updated 3.0 years ago by
ATpoint
82k • written 3.0 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
4.1k
views
Comment:
Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
3.0 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
3.0k
views
Comment:
Comment: Keep values from VCF file into Ensembl VEP annotation
3.0 years ago by
DareDevil
★ 4.3k
3
votes
2
replies
3.0k
views
Answer:
Answer: Keep values from VCF file into Ensembl VEP annotation
3.0 years ago by
DareDevil
★ 4.3k
2
votes
0
replies
742
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
2
votes
1
reply
2.5k
views
Answer:
Answer: Another infer_experiment.py interpretation question
18 months 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
Istvan Albert
100k • written 3.1 years ago by
DareDevil
★ 4.3k
2
votes
0
replies
5.2k
views
Comment:
Comment: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
3.1 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
1.7k
views
Comment:
Comment: Infering strand specificity of bam files using rseqc?
3.1 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
2.2k
views
Comment:
Comment: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approxima
3.1 years ago by
DareDevil
★ 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
0
votes
0
replies
3.2k
views
Comment:
Comment: Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at ap
3.1 years ago by
DareDevil
★ 4.3k
3
votes
0
replies
9.5k
views
Answer:
Answer: STAR alignment command.
3.1 years ago by
DareDevil
★ 4.3k
1
vote
1
reply
13k
views
Comment:
C: Bash scripting FastQC for multiple fastq files in multiple directories
3.1 years ago by
DareDevil
★ 4.3k
3
votes
1
reply
866
views
What should be the value of Sjdboverhang in STAR?
STAR
index
reference
sjdbOverhang
3.1 years ago by
DareDevil
★ 4.3k
5
votes
1
reply
13k
views
Answer:
A: Bash scripting FastQC for multiple fastq files in multiple directories
3.1 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
1.7k
views
Comment:
C: How to extract postions from gnomad using tabix?
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
Pierre Lindenbaum
161k • written 3.1 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
1.7k
views
Comment:
C: How to extract postions from gnomad using tabix?
3.1 years ago by
DareDevil
★ 4.3k
0
votes
1
reply
1.7k
views
Comment:
C: How to extract postions from gnomad using tabix?
3.1 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
4.1k
views
Comment:
C: How to convert gvcf file to normal vcf file ?
3.1 years ago by
DareDevil
★ 4.3k
5
votes
5
replies
4.1k
views
How to convert gvcf file to normal vcf file ?
vcf
gatk
gvcf
12 months ago by
DareDevil
★ 4.3k
2
votes
0
replies
679
views
Is it possible to apply limma on metabric data?
limma
metabric
mRNA
DEG
3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
1.7k
views
Comment:
C: LImma design matrix and contrast matrix creation
3.2 years ago by
DareDevil
★ 4.3k
1
vote
1
reply
1.7k
views
Comment:
C: LImma design matrix and contrast matrix creation
3.2 years ago by
DareDevil
★ 4.3k
0
votes
1
reply
2.9k
views
Comment:
C: How to get REF and ALT alleles from a genotype data?
3.2 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
5.3k
views
Comment:
C: Running VEP without --cache
3.2 years ago by
DareDevil
★ 4.3k
0
votes
1
reply
3.2k
views
Comment:
C: DEG analysis of METABRIC data from cBIOPORTAL
3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
2.5k
views
Comment:
C: CIBERSORT: Errors were encountered in input files, run aborted:
3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
2.5k
views
Comment:
C: CIBERSORT: Errors were encountered in input files, run aborted:
3.2 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
Ram
43k • written 3.2 years ago by
DareDevil
★ 4.3k
2
votes
0
replies
5.5k
views
Comment:
C: [mem_sam_pe] paired reads have different names. Without -p
3.2 years ago by
DareDevil
★ 4.3k
2
votes
0
replies
5.5k
views
Answer:
A: [mem_sam_pe] paired reads have different names. Without -p
3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
607
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
Ram
43k • written 3.2 years ago by
DareDevil
★ 4.3k
0
votes
1
reply
4.1k
views
Comment:
C: Are there any tutorials available for Nanostring data differential expression an
3.2 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
13k
views
Answer:
Answer: Bioinformatics Journal with no publishing fees?
updated 2.2 years ago by
Ram
43k • written 3.2 years ago by
DareDevil
★ 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
0
votes
0
replies
1.1k
views
Comment:
C: Agilent microarray data analysis end in no significant genes ?
3.2 years ago by
DareDevil
★ 4.3k
1
vote
1
reply
1.1k
views
Comment:
C: Agilent microarray data analysis end in no significant genes ?
3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
2.6k
views
Comment:
C: Batch correction in DESeq2---Normalized Counts
3.2 years ago by
DareDevil
★ 4.3k
2
votes
2
replies
688
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
0
votes
1
reply
1.1k
views
Comment:
C: Agilent microarray data analysis end in no significant genes ?
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
Kevin Blighe
87k • written 3.2 years ago by
DareDevil
★ 4.3k
0
votes
0
replies
622
views
How to perform relatedness across multiple trio cohort ?
trio
vcftools
relatedness
3.2 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
1.2k
views
Comment:
C: Download entire human rRNA sequences
3.2 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
1.2k
views
Comment:
C: Download entire human rRNA sequences
3.2 years ago by
DareDevil
★ 4.3k
1
vote
0
replies
1.1k
views
Comment:
C: A USER ERROR has occurred: Positive training model failed to converge.
3.3 years ago by
DareDevil
★ 4.3k
224 results • Page
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