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0
votes
0
replies
178
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
8 days ago by simplitia ▴ 130
0
votes
2
replies
845
views
scRNAseq: thoughts on merging datasets generating from different version of 10x cellranger?
scRNAseq Harmony 10x Seurat
updated 9 months ago by 6.5k • written 9 months ago by ▴ 130
0
votes
0
replies
822
views
Integration with Harmony using seurat object + SCTransform
SCTransform seurat scRNAseq
17 months ago by simplitia ▴ 130
3
votes
4
replies
866
views
How to tell if GEO SRA is paired or single?
rnaseq geo
18 months ago by simplitia ▴ 130
8
votes
6
replies
840
views
How many IGH genes are there? Confused about nomenclature.
rnaseq genecode
18 months ago by simplitia ▴ 130
0
votes
5
replies
2.2k
views
What are the units for the sctransform SCT scale.data slots?
10x Seurat scRNAseq
updated 21 months ago by 13k • written 21 months ago by ▴ 130
1
vote
2
replies
779
views
For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you recommend using raw or filtered matrix?
10x Seurat scRNAseq
22 months ago by simplitia ▴ 130
4
votes
3
replies
931
views
Create a bed file bins from fasta?
bed fasta
updated 23 months ago by 13k • written 23 months ago by ▴ 130
0
votes
4
replies
806
views
Biologically what does it mean when an exon has higher expression?
expression rnaseq gene
updated 2.0 years ago by 13k • written 2.0 years ago by ▴ 130
0
votes
0
replies
448
views
Can RNAseq expression be correlated with differential methylated regions?
rnaseq methylation
2.3 years ago by simplitia ▴ 130
1
vote
1
reply
545
views
What are the minimum packages required to compile samtools for Debian OS?
samtools
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 130
0
votes
8
replies
1.7k
views
Is there a way to safely remove all underscore from gene id for hg19 from genecode
rnaseq genecode
2.4 years ago by simplitia ▴ 130
0
votes
0
replies
486
views
Is there a Grange object for swiss-prot domain? What I want is to detect what domains are overlapping with genomic coordinates.
R
2.4 years ago by simplitia ▴ 130
0
votes
1
reply
652
views
Anyone know what the window size ( bin size) for dmrcate is?
EPIC 450K methylation
updated 2.4 years ago by ★ 2.0k • written 2.4 years ago by ▴ 130
0
votes
0
replies
639
views
Strelka2 stomatic calls, where is the GT tag ?
strelka annovar variant
2.8 years ago by simplitia ▴ 130
0
votes
1
reply
795
views
converting genomic version for annovar database?
annovar variant
updated 2.8 years ago by ▴ 580 • written 2.8 years ago by ▴ 130
7
votes
5
replies
1.6k
views
Is there a way to extract alignment score from STAR aligner bam files?
rnaseq
2.9 years ago by simplitia ▴ 130
0
votes
3
replies
1.3k
views
Extracting reads from fastq files with BBMAP?
bbmap fastq
updated 3.0 years ago by 142k • written 3.0 years ago by ▴ 130
1
vote
1
reply
747
views
Convert COSMIC VCF coordinates to that of ensembl format?
sequencing SNP alignment next-gen
3.5 years ago by simplitia ▴ 130
0
votes
0
replies
753
views
Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
RNA-Seq tcga rsem
3.8 years ago by simplitia ▴ 130
0
votes
5
replies
2.5k
views
Calculating and confirming shRNA knockdown gene from RNA-Seq?
RNA-Seq
updated 4.0 years ago by ▴ 850 • written 6.5 years ago by ▴ 130
1
vote
3
replies
1.3k
views
How reliable are the ensembl transcript isoforms?
RNA-Seq ensembl isoform
updated 4.1 years ago by ▴ 330 • written 4.1 years ago by ▴ 130
2
votes
1
reply
1.6k
views
GRanges: remove ranges that falls in between a larger range?
grange RNA-Seq r
updated 4.2 years ago by ▴ 40 • written 4.2 years ago by ▴ 130
1
vote
2
replies
1.6k
views
STAR: Is it ok to align with an index created from genecode but count features from gtf from ensembl?
RNA-Seq STAR alignment
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 130
0
votes
0
replies
557
views
How to interpret exon reads from recount for version 2?
RNA-Seq TCGA
4.7 years ago by simplitia ▴ 130
0
votes
0
replies
934
views
Advice for gene overlap with direction between two sets.
R chisquare statistics
5.0 years ago by simplitia ▴ 130
2
votes
3
replies
1.5k
views
Understanding FANTOM5 CAGE fields
RNA-Seq transcription tss
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 130
0
votes
1
reply
1.5k
views
Help convert GDC exploration url to API download?
gdc mutation portal
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 130
2
votes
4
replies
4.0k
views
How to recreate FASTQ from BAM
RNA-Seq BAM sequencing
updated 5.4 years ago by ▴ 310 • written 5.4 years ago by ▴ 130
10
votes
6
replies
3.7k
views
Hard time trying to calculate Allele Frequency and DP from Platypus
RNA-Seq SNV
updated 5.6 years ago by 87k • written 6.4 years ago by ▴ 130
2
votes
1
reply
1.8k
views
How to deconvolute whole blood and analyzed cell type separately for EWAS
methylation cpg 850K EPIC
updated 6.2 years ago by 87k • written 6.2 years ago by ▴ 130
1
vote
2
replies
2.4k
views
How to quantify PCR duplication from bam file
RNA-Seq
updated 6.3 years ago by 142k • written 6.3 years ago by ▴ 130
0
votes
8
replies
3.1k
views
Help with BWA: how to align paired as single and then combine again
RNA-Seq alignment bwa
6.4 years ago by simplitia ▴ 130
0
votes
0
replies
1.7k
views
Create fusion transcripts with breakpoint coordinates from two genes.
RNA-Seq sequence
8.1 years ago by simplitia ▴ 130
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