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1
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0
replies
624
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 3.1 years ago by ★ 4.3k
3
votes
2
replies
984
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 3.1 years ago by 82k • written 3.1 years ago by ★ 4.3k
1
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0
replies
4.1k
views
Comment: Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
3.1 years ago by DareDevil ★ 4.3k
1
vote
0
replies
3.0k
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Comment: Comment: Keep values from VCF file into Ensembl VEP annotation
3.1 years ago by DareDevil ★ 4.3k
3
votes
2
replies
3.0k
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Answer: Answer: Keep values from VCF file into Ensembl VEP annotation
3.1 years ago by DareDevil ★ 4.3k
2
votes
0
replies
745
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
3.1 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 100k • written 3.1 years ago by ★ 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
9.6k
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
873
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?
3.2 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 3.2 years ago by 161k • written 3.2 years ago by ★ 4.3k
0
votes
0
replies
1.7k
views
Comment: C: How to extract postions from gnomad using tabix?
3.2 years ago by DareDevil ★ 4.3k
0
votes
1
reply
1.7k
views
Comment: C: How to extract postions from gnomad using tabix?
3.2 years ago by DareDevil ★ 4.3k
0
votes
0
replies
4.1k
views
Comment: C: How to convert gvcf file to normal vcf file ?
3.2 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
682
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
3.0k
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
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0
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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 43k • written 3.2 years ago by ★ 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
609
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
4.2k
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
0
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1
reply
4.2k
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 2.3 years 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
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
696
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 ?
3.3 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 3.3 years ago by 87k • written 3.3 years ago by ★ 4.3k
0
votes
0
replies
626
views
How to perform relatedness across multiple trio cohort ?
trio vcftools relatedness
3.3 years ago by DareDevil ★ 4.3k
1
vote
0
replies
1.2k
views
Comment: C: Download entire human rRNA sequences
3.3 years ago by DareDevil ★ 4.3k
1
vote
0
replies
1.2k
views
Comment: C: Download entire human rRNA sequences
3.3 years ago by DareDevil ★ 4.3k
1
vote
0
replies
1.2k
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 3 of 5
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