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Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 2 days ago by ★ 2.4k • written 2 days ago by ▴ 110
3
votes
9
replies
2.5k
views
ChIP-Seq Analysis allele specific way?
ChIP-Seq ASE MACS2 VCF NGS
updated 3.6 years ago by ▴ 10 • written 5.3 years ago by ▴ 110
0
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1
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1.2k
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Does Nextera Transposase adapter sequence affects GATK HaplotypeCaller pipeline?
SNP GATK illumina RNA-Seq NGS
4.2 years ago by Susmita Mandal ▴ 110
0
votes
10
replies
3.9k
views
Split BAM file from paired end read into forward and reverse strand w.r.t reference genome
RNA-Seq NGS SNP Variant Calling samtools
updated 4.2 years ago by 82k • written 4.2 years ago by ▴ 110
0
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0
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517
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Tools and/or methods to detect allelic mapping bias.
RNA-Seq SNP variant calling ngs alelle specific
4.2 years ago by Susmita Mandal ▴ 110
0
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2
replies
1.8k
views
Splitting BAM file from paired end into forward and reverse strands?
RNA-Seq samtools ngs rna-seq VCF
4.3 years ago by Susmita Mandal ▴ 110
3
votes
10
replies
4.4k
views
Allele Specific Expression Analysis
SNP Allele specific RNA-Seq X chromosome STAR
updated 4.4 years ago by ▴ 340 • written 5.6 years ago by ▴ 110
1
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2
replies
1.4k
views
Outliers in a boxplot: Necessary or not?
RNA-Seq Statistics R
4.8 years ago by Susmita Mandal ▴ 110
0
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4
replies
1.4k
views
Moving average plot of gene expression ratio along the chromosome length
RNA-Seq R Bioconductor gene next-gen
4.9 years ago by Susmita Mandal ▴ 110
3
votes
4
replies
989
views
Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
RNA-Seq BAM SNP GATK Variant Calling
5.0 years ago by Susmita Mandal ▴ 110
1
vote
0
replies
893
views
Is it advisable to do allele specific expression analysis on single cell RNA-Seq data?
RNA-Seq Single-cell NGS ASE SNP
updated 5.1 years ago by 20 • written 5.1 years ago by ▴ 110
4
votes
12
replies
1.7k
views
Allele specific expression analysis using human cell line
RNA-Seq ASE NGS SNP Affimetrix
updated 5.1 years ago by ▴ 170 • written 5.2 years ago by ▴ 110
0
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0
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692
views
Genome Annotations? RepeatMasker class/family? Regulation?
RNA-Seq RepeatMasker Annotation NGS
5.2 years ago by Susmita Mandal ▴ 110
0
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2
replies
2.0k
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ChIP-Seq density plot of the TSS regions?
ChIP-Seq Deeptools Bedtools IGV ASE
updated 5.2 years ago by 19k • written 5.2 years ago by ▴ 110
2
votes
2
replies
10k
views
How to include genes having negative fold change in the log2 FC plot?
RNA-Seq log2 NGS fold change ASE
updated 5.2 years ago by 14k • written 5.2 years ago by ▴ 110
10
votes
13
replies
10k
views
8 follow
What is RPKM/FPKM > 1 or 3 or 5?
RNA-Seq rpkm fpkm normalization ngs
updated 2.0 years ago by • 0 • written 5.3 years ago by ▴ 110
2
votes
16
replies
6.2k
views
Converting Microarray SNP data into VCF format
Affymetrix SNP VCF RNA-Seq Microarray
updated 11 months ago by • 0 • written 5.3 years ago by ▴ 110
4
votes
4
replies
3.1k
views
coverage of a SNP site?
SNP coverage ASE bedtools ngs
updated 5.5 years ago by 87k • written 5.5 years ago by ▴ 110
0
votes
0
replies
1.4k
views
Normalization of read counts from HTSeq by library size
RNA-Seq HTSeq-count R NGS DESeq2
5.5 years ago by Susmita Mandal ▴ 110
0
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5
replies
2.7k
views
intersectBed a gtf file with a vcf file
intersectbed bedtools SNP
5.5 years ago by Susmita Mandal ▴ 110
0
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2
replies
1.3k
views
Reads that map to two different genomes, but with different map coordinates
BAM bamUtil bamUtil diff comparison NGS
5.6 years ago by Susmita Mandal ▴ 110
2
votes
12
replies
6.0k
views
LiftOver a VCF file
VCF Picard CrossMap LiftoverVcf
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 110
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