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5
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1
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1.4k
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Answer: Answer: RNA Seq HTSeq download GDC portal
2.6 years ago by DareDevil ★ 4.3k
1
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1
reply
7.9k
views
Comment: Comment: TCGA transcriptome data to R (DESeq2)
2.7 years ago by DareDevil ★ 4.3k
2
votes
0
replies
35k
views
Answer: Answer: Mapping Mouse gene names to Human gene names
2.7 years ago by DareDevil ★ 4.3k
22
votes
2
replies
1.8k
views
How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
VQSR GATK VariantRecalibrator
2.7 years ago by DareDevil ★ 4.3k
6
votes
0
replies
1.8k
views
Answer: Answer: How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
2.7 years ago by DareDevil ★ 4.3k
2
votes
0
replies
8.2k
views
Answer: Answer: Running featureCounts separately for each sample and merging results
2.8 years ago by DareDevil ★ 4.3k
5
votes
0
replies
7.4k
views
Answer: Answer: Split multiallelic SNPs to biallelic from vcf
2.8 years ago by DareDevil ★ 4.3k
3
votes
0
replies
5.8k
views
Comment: Comment: bcftools multiallelic split not working
2.8 years ago by DareDevil ★ 4.3k
2
votes
0
replies
535
views
How is the pvalue in cibersort calculated?
pvalue cibersort
2.9 years ago by DareDevil ★ 4.3k
2
votes
0
replies
18k
views
Comment: Comment: STAR align multiple files
3.2 years ago by DareDevil ★ 4.3k
1
vote
0
replies
5.0k
views
Comment: Comment: Aligning Multiple paired end files together
3.2 years ago by DareDevil ★ 4.3k
1
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1
reply
1.2k
views
Answer: Answer: METABRIC sample IDs
3.3 years ago by DareDevil ★ 4.3k
3
votes
1
reply
935
views
How to perform differential expression analysis of metabric data obtained from METABRIC?
DEseq2 cbioportal EdgeR limma
updated 3.4 years ago by ★ 1.6k • written 3.4 years ago by ★ 4.3k
0
votes
0
replies
852
views
Comment: Comment: How do I call compound hetrozygosity from multiple trios cohort?
3.4 years ago by DareDevil ★ 4.3k
2
votes
2
replies
852
views
How do I call compound hetrozygosity from multiple trios cohort?
ped gatk trio heterozygosity compound vcf
3.4 years ago by DareDevil ★ 4.3k
1
vote
0
replies
705
views
How to filter the germline INDELS?
INDELS GATK VCF
3.5 years ago by DareDevil ★ 4.3k
15
votes
4
replies
4.7k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 2.2 years ago by ▴ 190 • written 3.6 years ago by ★ 4.3k
3
votes
2
replies
1.1k
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 3.6 years ago by 85k • written 3.6 years ago by ★ 4.3k
1
vote
0
replies
4.7k
views
Comment: Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
3.6 years ago by DareDevil ★ 4.3k
1
vote
0
replies
3.3k
views
Comment: Comment: Keep values from VCF file into Ensembl VEP annotation
3.6 years ago by DareDevil ★ 4.3k
3
votes
2
replies
3.3k
views
Answer: Answer: Keep values from VCF file into Ensembl VEP annotation
3.6 years ago by DareDevil ★ 4.3k
2
votes
0
replies
830
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
3.6 years ago by DareDevil ★ 4.3k
2
votes
1
reply
2.9k
views
Answer: Answer: Another infer_experiment.py interpretation question
2.1 years ago by DareDevil ★ 4.3k
5
votes
2
replies
1.9k
views
Infering strand specificity of bam files using rseqc?
RSeQC bam featureCounts
updated 3.7 years ago by 102k • written 3.7 years ago by ★ 4.3k
2
votes
0
replies
5.6k
views
Comment: Comment: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
3.7 years ago by DareDevil ★ 4.3k
1
vote
0
replies
1.9k
views
Comment: Comment: Infering strand specificity of bam files using rseqc?
3.7 years ago by DareDevil ★ 4.3k
0
votes
0
replies
2.4k
views
Comment: Comment: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approxima
3.7 years ago by DareDevil ★ 4.3k
4
votes
2
replies
2.4k
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable vcf gatk
3.7 years ago by DareDevil ★ 4.3k
0
votes
0
replies
3.7k
views
Comment: Comment: Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at ap
3.7 years ago by DareDevil ★ 4.3k
3
votes
0
replies
10k
views
Answer: Answer: STAR alignment command.
3.7 years ago by DareDevil ★ 4.3k
1
vote
1
reply
15k
views
Comment: C: Bash scripting FastQC for multiple fastq files in multiple directories
3.7 years ago by DareDevil ★ 4.3k
3
votes
1
reply
988
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
3.7 years ago by DareDevil ★ 4.3k
5
votes
1
reply
15k
views
Answer: A: Bash scripting FastQC for multiple fastq files in multiple directories
3.7 years ago by DareDevil ★ 4.3k
0
votes
0
replies
1.9k
views
Comment: C: How to extract postions from gnomad using tabix?
3.7 years ago by DareDevil ★ 4.3k
7
votes
7
replies
1.9k
views
How to extract postions from gnomad using tabix?
tabix gnomad vcf
updated 3.7 years ago by 164k • written 3.7 years ago by ★ 4.3k
0
votes
0
replies
1.9k
views
Comment: C: How to extract postions from gnomad using tabix?
3.7 years ago by DareDevil ★ 4.3k
0
votes
1
reply
1.9k
views
Comment: C: How to extract postions from gnomad using tabix?
3.7 years ago by DareDevil ★ 4.3k
0
votes
0
replies
4.9k
views
Comment: C: How to convert gvcf file to normal vcf file ?
3.7 years ago by DareDevil ★ 4.3k
6
votes
5
replies
4.9k
views
How to convert gvcf file to normal vcf file ?
vcf gatk gvcf
19 months ago by DareDevil ★ 4.3k
2
votes
0
replies
769
views
Is it possible to apply limma on metabric data?
limma metabric mRNA DEG
3.7 years ago by DareDevil ★ 4.3k
0
votes
0
replies
2.1k
views
Comment: C: LImma design matrix and contrast matrix creation
3.8 years ago by DareDevil ★ 4.3k
1
vote
1
reply
2.1k
views
Comment: C: LImma design matrix and contrast matrix creation
3.8 years ago by DareDevil ★ 4.3k
0
votes
1
reply
3.4k
views
Comment: C: How to get REF and ALT alleles from a genotype data?
3.8 years ago by DareDevil ★ 4.3k
1
vote
0
replies
5.9k
views
Comment: C: Running VEP without --cache
3.8 years ago by DareDevil ★ 4.3k
0
votes
1
reply
3.6k
views
Comment: C: DEG analysis of METABRIC data from cBIOPORTAL
3.8 years ago by DareDevil ★ 4.3k
0
votes
0
replies
2.7k
views
Comment: C: CIBERSORT: Errors were encountered in input files, run aborted:
3.8 years ago by DareDevil ★ 4.3k
0
votes
0
replies
2.7k
views
Comment: C: CIBERSORT: Errors were encountered in input files, run aborted:
3.8 years ago by DareDevil ★ 4.3k
2
votes
4
replies
2.7k
views
CIBERSORT: Errors were encountered in input files, run aborted:
deconvolution cibersort
updated 20 months ago by 44k • written 3.8 years ago by ★ 4.3k
2
votes
0
replies
6.0k
views
Comment: C: [mem_sam_pe] paired reads have different names. Without -p
3.8 years ago by DareDevil ★ 4.3k
2
votes
0
replies
6.0k
views
Answer: A: [mem_sam_pe] paired reads have different names. Without -p
3.8 years ago by DareDevil ★ 4.3k
239 results • Page 3 of 5
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