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questions
0
votes
0
replies
199
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
25 days ago by
simplitia
▴ 130
0
votes
2
replies
860
views
scRNAseq: thoughts on merging datasets generating from different version of 10x cellranger?
scRNAseq
Harmony
10x
Seurat
updated 10 months ago by
Rob
6.6k • written 10 months ago by
simplitia
▴ 130
0
votes
0
replies
846
views
Integration with Harmony using seurat object + SCTransform
SCTransform
seurat
scRNAseq
17 months ago by
simplitia
▴ 130
3
votes
4
replies
889
views
How to tell if GEO SRA is paired or single?
rnaseq
geo
18 months ago by
simplitia
▴ 130
8
votes
6
replies
854
views
How many IGH genes are there? Confused about nomenclature.
rnaseq
genecode
19 months ago by
simplitia
▴ 130
0
votes
5
replies
2.3k
views
What are the units for the sctransform SCT scale.data slots?
10x
Seurat
scRNAseq
updated 22 months ago by
rpolicastro
13k • written 22 months ago by
simplitia
▴ 130
1
vote
2
replies
787
views
For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you recommend using raw or filtered matrix?
10x
Seurat
scRNAseq
23 months ago by
simplitia
▴ 130
4
votes
3
replies
944
views
Create a bed file bins from fasta?
bed
fasta
updated 23 months ago by
rpolicastro
13k • written 23 months ago by
simplitia
▴ 130
0
votes
4
replies
818
views
Biologically what does it mean when an exon has higher expression?
expression
rnaseq
gene
updated 2.0 years ago by
rpolicastro
13k • written 2.0 years ago by
simplitia
▴ 130
0
votes
0
replies
450
views
Can RNAseq expression be correlated with differential methylated regions?
rnaseq
methylation
2.4 years ago by
simplitia
▴ 130
1
vote
1
reply
548
views
What are the minimum packages required to compile samtools for Debian OS?
samtools
updated 2.4 years ago by
Mensur Dlakic
★ 27k • written 2.4 years ago by
simplitia
▴ 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
491
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
658
views
Anyone know what the window size ( bin size) for dmrcate is?
EPIC
450K
methylation
updated 2.4 years ago by
Basti
★ 2.0k • written 2.4 years ago by
simplitia
▴ 130
0
votes
0
replies
647
views
Strelka2 stomatic calls, where is the GT tag ?
strelka
annovar
variant
2.8 years ago by
simplitia
▴ 130
0
votes
1
reply
808
views
converting genomic version for annovar database?
annovar
variant
updated 2.8 years ago by
Jianyu
▴ 580 • written 2.8 years ago by
simplitia
▴ 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
1.4k
views
Extracting reads from fastq files with BBMAP?
bbmap
fastq
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
simplitia
▴ 130
1
vote
1
reply
752
views
Convert COSMIC VCF coordinates to that of ensembl format?
sequencing
SNP
alignment
next-gen
3.6 years ago by
simplitia
▴ 130
0
votes
0
replies
759
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
rohitsatyam102
▴ 870 • written 6.6 years ago by
simplitia
▴ 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
Astrid_Ensembl
▴ 330 • written 4.1 years ago by
simplitia
▴ 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
Strand NGS
▴ 40 • written 4.2 years ago by
simplitia
▴ 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
Kristoffer Vitting-Seerup
★ 4.1k • written 4.6 years ago by
simplitia
▴ 130
0
votes
0
replies
562
views
How to interpret exon reads from recount for version 2?
RNA-Seq
TCGA
4.8 years ago by
simplitia
▴ 130
0
votes
0
replies
935
views
Advice for gene overlap with direction between two sets.
R
chisquare
statistics
5.1 years ago by
simplitia
▴ 130
2
votes
3
replies
1.5k
views
Understanding FANTOM5 CAGE fields
RNA-Seq
transcription
tss
updated 5.3 years ago by
Kristoffer Vitting-Seerup
★ 4.1k • written 5.3 years ago by
simplitia
▴ 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
Biostar
20 • written 5.4 years ago by
simplitia
▴ 130
2
votes
4
replies
4.1k
views
How to recreate FASTQ from BAM
RNA-Seq
BAM
sequencing
updated 5.4 years ago by
ctseto
▴ 310 • written 5.4 years ago by
simplitia
▴ 130
10
votes
6
replies
3.8k
views
Hard time trying to calculate Allele Frequency and DP from Platypus
RNA-Seq
SNV
updated 5.7 years ago by
Kevin Blighe
88k • written 6.4 years ago by
simplitia
▴ 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 6.3 years ago by
Kevin Blighe
88k • written 6.3 years ago by
simplitia
▴ 130
1
vote
2
replies
2.4k
views
How to quantify PCR duplication from bam file
RNA-Seq
updated 6.4 years ago by
GenoMax
142k • written 6.4 years ago by
simplitia
▴ 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
6.5 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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