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4
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0
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21k
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Answer: Answer: TrimGalore! on multiple paired fastq files
3.1 years ago by DareDevil ★ 4.4k
0
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1
reply
3.3k
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Comment: Comment: Problem creating new conda environment
3.1 years ago by DareDevil ★ 4.4k
2
votes
1
reply
19k
views
Comment: Comment: How to do FPKM differential analysis?
3.2 years ago by DareDevil ★ 4.4k
1
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0
replies
14k
views
Comment: Comment: How to change color of rownames display in pheatmap
3.2 years ago by DareDevil ★ 4.4k
3
votes
2
replies
1.5k
views
A USER ERROR has occurred: Positive training model failed to converge.
gatk vcf max-gaussians
updated 3.2 years ago by • 0 • written 4.8 years ago by ★ 4.4k
1
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0
replies
1.4k
views
Comment: Comment: The difference of RNA-seq data between TCGA and ENCODE
3.3 years ago by DareDevil ★ 4.4k
1
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1
reply
1.4k
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Comment: Comment: The difference of RNA-seq data between TCGA and ENCODE
3.3 years ago by DareDevil ★ 4.4k
3
votes
1
reply
9.8k
views
Comment: Comment: TCGA transcriptome data to R (DESeq2)
3.4 years ago by DareDevil ★ 4.4k
2
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0
replies
11k
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Comment: Comment: How to extract count matrix from TCGAbiolinks using STAR-Counts
3.5 years ago by DareDevil ★ 4.4k
5
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1
reply
2.0k
views
Answer: Answer: RNA Seq HTSeq download GDC portal
3.6 years ago by DareDevil ★ 4.4k
1
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1
reply
9.8k
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Comment: Comment: TCGA transcriptome data to R (DESeq2)
3.6 years ago by DareDevil ★ 4.4k
2
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0
replies
42k
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Answer: Answer: Mapping Mouse gene names to Human gene names
3.6 years ago by DareDevil ★ 4.4k
22
votes
2
replies
2.2k
views
How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
VQSR GATK VariantRecalibrator
3.7 years ago by DareDevil ★ 4.4k
6
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0
replies
2.2k
views
Answer: Answer: How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
3.7 years ago by DareDevil ★ 4.4k
2
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0
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11k
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Answer: Answer: Running featureCounts separately for each sample and merging results
3.7 years ago by DareDevil ★ 4.4k
5
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0
replies
8.7k
views
Answer: Answer: Split multiallelic SNPs to biallelic from vcf
3.8 years ago by DareDevil ★ 4.4k
3
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0
replies
8.5k
views
Comment: Comment: bcftools multiallelic split not working
3.8 years ago by DareDevil ★ 4.4k
2
votes
0
replies
729
views
How is the pvalue in cibersort calculated?
pvalue cibersort
3.9 years ago by DareDevil ★ 4.4k
2
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0
replies
20k
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Comment: Comment: STAR align multiple files
4.2 years ago by DareDevil ★ 4.4k
1
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0
replies
5.9k
views
Comment: Comment: Aligning Multiple paired end files together
4.2 years ago by DareDevil ★ 4.4k
1
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1
reply
1.6k
views
Answer: Answer: METABRIC sample IDs
4.3 years ago by DareDevil ★ 4.4k
3
votes
1
reply
1.2k
views
How to perform differential expression analysis of metabric data obtained from METABRIC?
DEseq2 cbioportal EdgeR limma
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by ★ 4.4k
0
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0
replies
1.1k
views
Comment: Comment: How do I call compound hetrozygosity from multiple trios cohort?
4.4 years ago by DareDevil ★ 4.4k
2
votes
2
replies
1.1k
views
How do I call compound hetrozygosity from multiple trios cohort?
ped gatk trio heterozygosity compound vcf
4.4 years ago by DareDevil ★ 4.4k
1
vote
0
replies
861
views
How to filter the germline INDELS?
INDELS GATK VCF
4.4 years ago by DareDevil ★ 4.4k
17
votes
4
replies
6.0k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 3.1 years ago by ▴ 250 • written 4.6 years ago by ★ 4.4k
3
votes
2
replies
1.7k
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 4.6 years ago by 89k • written 4.6 years ago by ★ 4.4k
1
vote
0
replies
6.0k
views
Comment: Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
4.6 years ago by DareDevil ★ 4.4k
1
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0
replies
4.1k
views
Comment: Comment: Keep values from VCF file into Ensembl VEP annotation
4.6 years ago by DareDevil ★ 4.4k
3
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2
replies
4.1k
views
Answer: Answer: Keep values from VCF file into Ensembl VEP annotation
4.6 years ago by DareDevil ★ 4.4k
2
votes
0
replies
1.0k
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
4.6 years ago by DareDevil ★ 4.4k
2
votes
1
reply
4.0k
views
Answer: Answer: Another infer_experiment.py interpretation question
3.0 years ago by DareDevil ★ 4.4k
5
votes
2
replies
2.5k
views
Infering strand specificity of bam files using rseqc?
RSeQC bam featureCounts
updated 4.6 years ago by 103k • written 4.6 years ago by ★ 4.4k
2
votes
0
replies
6.8k
views
Comment: Comment: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
4.6 years ago by DareDevil ★ 4.4k
1
vote
0
replies
2.5k
views
Comment: Comment: Infering strand specificity of bam files using rseqc?
4.6 years ago by DareDevil ★ 4.4k
0
votes
0
replies
2.7k
views
Comment: Comment: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approxima
4.6 years ago by DareDevil ★ 4.4k
4
votes
2
replies
2.7k
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable vcf gatk
4.6 years ago by DareDevil ★ 4.4k
0
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0
replies
4.7k
views
Comment: Comment: Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at ap
4.6 years ago by DareDevil ★ 4.4k
3
votes
0
replies
11k
views
Answer: Answer: STAR alignment command.
4.6 years ago by DareDevil ★ 4.4k
1
vote
1
reply
17k
views
Comment: C: Bash scripting FastQC for multiple fastq files in multiple directories
4.6 years ago by DareDevil ★ 4.4k
3
votes
1
reply
1.4k
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
4.6 years ago by DareDevil ★ 4.4k
5
votes
1
reply
17k
views
Answer: A: Bash scripting FastQC for multiple fastq files in multiple directories
4.6 years ago by DareDevil ★ 4.4k
0
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0
replies
2.5k
views
Comment: C: How to extract postions from gnomad using tabix?
4.6 years ago by DareDevil ★ 4.4k
7
votes
7
replies
2.5k
views
How to extract postions from gnomad using tabix?
tabix gnomad vcf
updated 4.6 years ago by 166k • written 4.6 years ago by ★ 4.4k
0
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0
replies
2.5k
views
Comment: C: How to extract postions from gnomad using tabix?
4.6 years ago by DareDevil ★ 4.4k
0
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1
reply
2.5k
views
Comment: C: How to extract postions from gnomad using tabix?
4.6 years ago by DareDevil ★ 4.4k
0
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0
replies
6.4k
views
Comment: C: How to convert gvcf file to normal vcf file ?
4.6 years ago by DareDevil ★ 4.4k
6
votes
5
replies
6.4k
views
How to convert gvcf file to normal vcf file ?
vcf gatk gvcf
2.5 years ago by DareDevil ★ 4.4k
2
votes
0
replies
961
views
Is it possible to apply limma on metabric data?
limma metabric mRNA DEG
4.7 years ago by DareDevil ★ 4.4k
0
votes
0
replies
3.0k
views
Comment: C: LImma design matrix and contrast matrix creation
4.7 years ago by DareDevil ★ 4.4k
248 results • Page 3 of 5
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