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4
votes
6
replies
924
views
10x Cellranger SN RNA-seq BAM file output looks off
cellranger samtools star bam rna-seq
updated 13 months ago by 43k • written 13 months ago by ▴ 60
2
votes
2
replies
626
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
updated 10 months ago by 43k • written 13 months ago by ▴ 60
1
vote
1
reply
894
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
votes
3
replies
994
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 2.2 years ago by 4.2k • written 2.2 years ago by ▴ 60
0
votes
2
replies
692
views
Ensembl variant consequences and classification info in table format
SO Ensembl API
2.5 years ago by rebeliscu ▴ 60
0
votes
0
replies
592
views
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
replies
692
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
10
votes
8
replies
3.1k
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
votes
3
replies
780
views
Exome sequencing one sample on two lanes considered two read groups for marking of PCR duplicates?
deduplication read groups exome sequencing
updated 2.6 years ago by 142k • written 2.6 years ago by ▴ 60
2
votes
8
replies
2.4k
views
BBDuk quality filtering not producing expected results
filtering trimming QC BBDuk quality
updated 2.6 years ago by 35k • written 2.6 years ago by ▴ 60
0
votes
0
replies
425
views
TCGA Agilent level 2 to level 3
TCGA
2.7 years ago by rebeliscu ▴ 60
2
votes
3
replies
1.3k
views
GDC RNA-seq pipeline: Original vs. Dr15plus?
RNA-seq GDC
updated 2.7 years ago by ★ 1.2k • written 2.7 years ago by ▴ 60
0
votes
0
replies
548
views
Where to find TCGA hg38 WXS coverage per sample
TCGA WXS coverage
3.0 years ago by rebeliscu ▴ 60
1
vote
2
replies
4.8k
views
fastq.gz unexpected end of file: Can this be fixed?
corrup fastq
updated 3.0 years ago by 142k • written 3.0 years ago by ▴ 60
1
vote
2
replies
1.6k
views
Where to install latest Affymetrix Power Tools?
affymetrix
updated 3.1 years ago by 142k • written 3.1 years ago by ▴ 60
1
vote
2
replies
1.4k
views
RNA-seq data: Contradictory counts vs. variance/dispersion trend?
RNA-Seq rna-seq
updated 3.7 years ago by 87k • written 3.7 years ago by ▴ 60
0
votes
0
replies
976
views
"Manual" enrichment analysis of gene set for genes associated with cell types
RNA-Seq deseq2 gene enrichment analysis gsea
5.2 years ago by rebeliscu ▴ 60
17 results • Page 1 of 1
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