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Comment: Comment: 10x Cellranger SN RNA-seq BAM file output looks off
12 months ago by rebeliscu ▴ 60
0
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0
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884
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Comment: Comment: 10x Cellranger SN RNA-seq BAM file output looks off
12 months ago by rebeliscu ▴ 60
4
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6
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884
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10x Cellranger SN RNA-seq BAM file output looks off
cellranger samtools star bam rna-seq
updated 12 months ago by 43k • written 12 months ago by ▴ 60
0
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0
replies
602
views
Comment: Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
12 months ago by rebeliscu ▴ 60
2
votes
2
replies
602
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
updated 10 months ago by 43k • written 12 months ago by ▴ 60
1
vote
1
reply
872
views
BCFtools for somatic vs. germline variant calling
germline-variant bcftools somatic-variant RNA-seq
updated 13 months ago by 43k • written 13 months ago by ▴ 60
0
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1
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975
views
Comment: Comment: How to normalize and batch correct SC RNA-seq data from multiple libraries and c
2.1 years ago by rebeliscu ▴ 60
0
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3
replies
975
views
How to normalize and batch correct SC RNA-seq data from multiple libraries and confounded with biological differences
batch RNA-seq normalization preprocessing single-cell
updated 2.1 years ago by 4.2k • written 2.1 years ago by ▴ 60
0
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0
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679
views
Comment: Comment: Ensembl variant consequences and classification info in table format
2.4 years ago by rebeliscu ▴ 60
0
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2
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679
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Ensembl variant consequences and classification info in table format
SO Ensembl API
2.4 years ago by rebeliscu ▴ 60
0
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0
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583
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VEP: "Given ref" field is empty when a ref. allele was in VCF input
WXS VCF VEP
2.5 years ago by rebeliscu ▴ 60
1
vote
0
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684
views
Qualimap whole exome sequencing depth of coverage - use whole genome or exome as reference?
coverage wxs qualimap depth
2.5 years ago by rebeliscu ▴ 60
1
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0
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3.0k
views
Comment: Comment: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
2.5 years ago by rebeliscu ▴ 60
0
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1
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3.0k
views
Comment: Comment: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
2.5 years ago by rebeliscu ▴ 60
10
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8
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3.0k
views
Base recalibration in normal vs. tumor somatic variant calling in WXS data?
WXS recalibration variant somatic
updated 8 months ago by ▴ 70 • written 2.5 years ago by ▴ 60
0
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1
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3.0k
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Comment: Comment: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
2.5 years ago by rebeliscu ▴ 60
0
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1
reply
766
views
Comment: Comment: Exome sequencing one sample on two lanes considered two read groups for marking
2.5 years ago by rebeliscu ▴ 60
0
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3
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766
views
Exome sequencing one sample on two lanes considered two read groups for marking of PCR duplicates?
deduplication read groups exome sequencing
updated 2.5 years ago by 141k • written 2.5 years ago by ▴ 60
0
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0
replies
2.3k
views
Comment: Comment: BBDuk quality filtering not producing expected results
2.5 years ago by rebeliscu ▴ 60
0
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1
reply
2.3k
views
Comment: Comment: BBDuk quality filtering not producing expected results
2.5 years ago by rebeliscu ▴ 60
0
votes
1
reply
2.3k
views
Comment: Comment: BBDuk quality filtering not producing expected results
2.5 years ago by rebeliscu ▴ 60
2
votes
8
replies
2.3k
views
BBDuk quality filtering not producing expected results
filtering trimming QC BBDuk quality
updated 2.5 years ago by 35k • written 2.5 years ago by ▴ 60
0
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1
reply
2.3k
views
Comment: Comment: BBDuk quality filtering not producing expected results
2.5 years ago by rebeliscu ▴ 60
0
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0
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418
views
TCGA Agilent level 2 to level 3
TCGA
2.7 years ago by rebeliscu ▴ 60
0
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0
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1.3k
views
Comment: Comment: GDC RNA-seq pipeline: Original vs. Dr15plus?
2.7 years ago by rebeliscu ▴ 60
2
votes
3
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1.3k
views
GDC RNA-seq pipeline: Original vs. Dr15plus?
RNA-seq GDC
updated 2.6 years ago by ★ 1.2k • written 2.7 years ago by ▴ 60
0
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1
reply
54k
views
Comment: Comment: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Ge
2.9 years ago by rebeliscu ▴ 60
0
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0
replies
538
views
Where to find TCGA hg38 WXS coverage per sample
TCGA WXS coverage
2.9 years ago by rebeliscu ▴ 60
1
vote
2
replies
4.7k
views
fastq.gz unexpected end of file: Can this be fixed?
corrup fastq
updated 2.9 years ago by 141k • written 2.9 years ago by ▴ 60
1
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2
replies
1.6k
views
Where to install latest Affymetrix Power Tools?
affymetrix
updated 3.0 years ago by 141k • written 3.0 years ago by ▴ 60
0
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0
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1.4k
views
Comment: C: RNA-seq data: Contradictory counts vs. variance/dispersion trend?
3.6 years ago by rebeliscu ▴ 60
1
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2
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1.4k
views
RNA-seq data: Contradictory counts vs. variance/dispersion trend?
RNA-Seq rna-seq
updated 3.6 years ago by 87k • written 3.6 years ago by ▴ 60
0
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1
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2.1k
views
Comment: A: Small dispersion values in differential expression analysis
3.6 years ago by rebeliscu ▴ 60
0
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0
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969
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"Manual" enrichment analysis of gene set for genes associated with cell types
RNA-Seq deseq2 gene enrichment analysis gsea
5.1 years ago by rebeliscu ▴ 60
0
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0
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3.4k
views
Comment: Comment: WGCNA for less than 15 samples
updated 18 months ago by 43k • written 5.2 years ago by ▴ 60
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