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11k
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Comment: Comment: STAR align multiple files
7 weeks ago by dare_devil ★ 1.5k
0
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0
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2.3k
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Comment: Comment: Aligning Multiple paired end files together
7 weeks ago by dare_devil ★ 1.5k
0
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0
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246
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Comment: Comment: METABRIC sample IDs
3 months ago by dare_devil ★ 1.5k
1
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1
reply
227
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How to perform differential expression analysis of metabric data obtained from METABRIC?
DEseq2 cbioportal EdgeR limma
updated 3 months ago by ★ 1.1k • written 3 months ago by ★ 1.5k
0
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0
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205
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Comment: Comment: How do I call compound hetrozygosity from multiple trios cohort?
4 months ago by dare_devil ★ 1.5k
0
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2
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205
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How do I call compound hetrozygosity from multiple trios cohort?
ped gatk trio heterozygosity compound vcf
4 months ago by dare_devil ★ 1.5k
0
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0
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127
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How to filter the germline INDELS?
INDELS GATK VCF
5 months ago by dare_devil ★ 1.5k
10
votes
3
replies
903
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 6 months ago by ▴ 120 • written 6 months ago by ★ 1.5k
1
vote
2
replies
394
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 6 months ago by 55k • written 6 months ago by ★ 1.5k
0
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0
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903
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Comment: Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
6 months ago by dare_devil ★ 1.5k
0
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0
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891
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Comment: Comment: Keep values from VCF file into Ensembl VEP annotation
6 months ago by dare_devil ★ 1.5k
1
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1
reply
891
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Answer: Answer: Keep values from VCF file into Ensembl VEP annotation
6 months ago by dare_devil ★ 1.5k
0
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0
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193
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what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
6 months ago by dare_devil ★ 1.5k
0
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1
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596
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Answer: Answer: Another infer_experiment.py interpretation question
6 months ago by dare_devil ★ 1.5k
2
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2
replies
507
views
Infering strand specificity of bam files using rseqc?
RSeQC bam featureCounts
updated 7 months ago by 90k • written 7 months ago by ★ 1.5k
0
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0
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3.4k
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Comment: Comment: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
7 months ago by dare_devil ★ 1.5k
0
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0
replies
507
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Comment: Comment: Infering strand specificity of bam files using rseqc?
7 months ago by dare_devil ★ 1.5k
0
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0
replies
952
views
Comment: Comment: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approxima
7 months ago by dare_devil ★ 1.5k
1
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2
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952
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable vcf gatk
7 months ago by dare_devil ★ 1.5k
0
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0
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604
views
Comment: Comment: Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at ap
7 months ago by dare_devil ★ 1.5k
1
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0
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6.3k
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Answer: Answer: STAR alignment command.
7 months ago by dare_devil ★ 1.5k
0
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1
reply
6.8k
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Comment: C: Bash scripting FastQC for multiple fastq files in multiple directories
7 months ago by dare_devil ★ 1.5k
0
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1
reply
264
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
7 months ago by dare_devil ★ 1.5k
1
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1
reply
6.8k
views
Answer: A: Bash scripting FastQC for multiple fastq files in multiple directories
7 months ago by dare_devil ★ 1.5k
0
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0
replies
541
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Comment: C: How to extract postions from gnomad using tabix?
7 months ago by dare_devil ★ 1.5k
5
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7
replies
541
views
How to extract postions from gnomad using tabix?
tabix gnomad vcf
updated 7 months ago by 139k • written 7 months ago by ★ 1.5k
0
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0
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541
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Comment: C: How to extract postions from gnomad using tabix?
7 months ago by dare_devil ★ 1.5k
0
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1
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541
views
Comment: C: How to extract postions from gnomad using tabix?
7 months ago by dare_devil ★ 1.5k
0
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0
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659
views
Comment: C: How to convert gvcf file to normal vcf file ?
7 months ago by dare_devil ★ 1.5k
5
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5
replies
659
views
How to convert gvcf file to normal vcf file ?
gatk vcf gvcf
updated 7 months ago by ▴ 610 • written 7 months ago by ★ 1.5k
0
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0
replies
261
views
Is it possible to apply limma on metabric data?
limma metabric mRNA DEG
8 months ago by dare_devil ★ 1.5k
0
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0
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386
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Comment: C: LImma design matrix and contrast matrix creation
8 months ago by dare_devil ★ 1.5k
0
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1
reply
386
views
Comment: C: LImma design matrix and contrast matrix creation
8 months ago by dare_devil ★ 1.5k
0
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1
reply
508
views
Comment: C: How to get REF and ALT alleles from a genotype data?
8 months ago by dare_devil ★ 1.5k
0
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0
replies
1.9k
views
Comment: C: Running VEP without --cache
8 months ago by dare_devil ★ 1.5k
0
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1
reply
1.9k
views
Comment: C: DEG analysis of METABRIC data from cBIOPORTAL
8 months ago by dare_devil ★ 1.5k
0
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0
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569
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Comment: C: CIBERSORT: Errors were encountered in input files, run aborted:
8 months ago by dare_devil ★ 1.5k
0
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0
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569
views
Comment: C: CIBERSORT: Errors were encountered in input files, run aborted:
8 months ago by dare_devil ★ 1.5k
0
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4
replies
569
views
CIBERSORT: Errors were encountered in input files, run aborted:
bioinformatics deconvolution cibersort
12 weeks ago by dare_devil ★ 1.5k
0
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0
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3.1k
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Comment: C: [mem_sam_pe] paired reads have different names. Without -p
8 months ago by dare_devil ★ 1.5k
0
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0
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3.1k
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Answer: A: [mem_sam_pe] paired reads have different names. Without -p
8 months ago by dare_devil ★ 1.5k
0
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0
replies
235
views
What is the cut off used in TCGA vcf files for allelic frequency for calling it as somatic?
tcga vcf
8 months ago by dare_devil ★ 1.5k
4
votes
4
replies
977
views
Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?
tutorial nanostring deseq2 limma
updated 6 months ago by ▴ 180 • written 8 months ago by ★ 1.5k
0
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1
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977
views
Comment: C: Are there any tutorials available for Nanostring data differential expression an
8 months ago by dare_devil ★ 1.5k
0
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0
replies
10.0k
views
Answer: A: Bioinformatics Journal with no publishing fees?
8 months ago by dare_devil ★ 1.5k
1
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1
reply
296
views
Are there any repository for panel of normal for running Mutect2?
Mutect2 PON panel of normal gatk
8 months ago by dare_devil ★ 1.5k
0
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0
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354
views
Comment: C: Agilent microarray data analysis end in no significant genes ?
8 months ago by dare_devil ★ 1.5k
0
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1
reply
354
views
Comment: C: Agilent microarray data analysis end in no significant genes ?
8 months ago by dare_devil ★ 1.5k
0
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0
replies
412
views
Comment: C: Batch correction in DESeq2---Normalized Counts
8 months ago by dare_devil ★ 1.5k
0
votes
2
replies
256
views
What test can be conducted to check ratio between the groups are significant ?
pvalue statistical test p-value cibersort
8 months ago by dare_devil ★ 1.5k
132 results • Page 1 of 3
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