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Showing :
questions
2
votes
3
replies
1.3k
views
how can I get the coverage over introns only in a RNA-seq experiment?
RNA-Seq
coverage
introns
5.5 years ago by
Lila M
★ 1.2k
48
votes
14
replies
21k
views
8 follow
should I merge fastq files for different lanes before do QC?
RNA-Seq
merge
QC
updated 5.6 years ago by
blueskypie
▴ 70 • written 6.6 years ago by
Lila M
★ 1.2k
9
votes
9
replies
3.2k
views
Problems running variant calling (VC) GATK: SAM/BAM/CRAM file dedup.bam is malformed
GATK
VC
RNA-Seq
5.6 years ago by
Lila M
★ 1.2k
20
votes
15
replies
1.7k
views
How can I get only the rows when for the converge points : - +
R
convergence points
updated 5.7 years ago by
Alex Reynolds
35k • written 5.7 years ago by
Lila M
★ 1.2k
2
votes
2
replies
1.4k
views
what scale does multiBigwigSummary use for score
multiBigwigSummary
deepTools
score
updated 5.7 years ago by
Devon Ryan
104k • written 5.7 years ago by
Lila M
★ 1.2k
1
vote
2
replies
1.2k
views
Is possible to quantify the RNAPOLII levels on all the annotated genes using biwgiw files?
bigwig
annotation
quantification
RNAPOL
updated 5.7 years ago by
venu
7.1k • written 5.7 years ago by
Lila M
★ 1.2k
0
votes
0
replies
838
views
Does any one know how this Percentage-normalized Signal has been calculated?
repli-seq
ucsc-tables
ucsc
5.8 years ago by
Lila M
★ 1.2k
4
votes
1
reply
7.0k
views
How can I analyze more than two conditions in DESeq2?
RNA-Seq
DESeq2
updated 5.9 years ago by
Lisa Ha
▴ 120 • written 5.9 years ago by
Lila M
★ 1.2k
10
votes
7
replies
3.9k
views
Is possible to convert BSgenome object to GRange?
BSgenome
GRanges
updated 6.3 years ago by
Devon Ryan
104k • written 6.3 years ago by
Lila M
★ 1.2k
27
votes
33
replies
17k
views
high % of reads mapped to multiple loci after STAR mapping
RNA-Seq
STAR
single-end
updated 6.4 years ago by
Hussain Ather
▴ 990 • written 6.4 years ago by
Lila M
★ 1.2k
5
votes
12
replies
5.7k
views
Should I remove all the overrepresented sequences to improve GC content in fastqc?
fastqc
RNA-Seq
single-end
overrepresented
6.4 years ago by
Lila M
★ 1.2k
2
votes
4
replies
1.5k
views
Any workshop in Europe related with advance genome biology and Perl (or R or python)
workshop
genome
perl
python
R
6.4 years ago by
Lila M
★ 1.2k
2
votes
4
replies
2.1k
views
is always necessary to do an intermediate index generations and 2nd pass alignment with STAR?
RNAseq
alignment
index
STAR
updated 6.5 years ago by
arta
▴ 670 • written 6.5 years ago by
Lila M
★ 1.2k
4
votes
13
replies
4.3k
views
Illumina NextSeq 500/550: PE or SE for ChIP seq and coverage?
paired-end
single-end
sequencing
library
updated 6.5 years ago by
Devon Ryan
104k • written 6.5 years ago by
Lila M
★ 1.2k
2
votes
6
replies
1.7k
views
Error when run testForDEU DEXSeq
DEXSeq
error
DEU
RNAseq
6.5 years ago by
Lila M
★ 1.2k
6
votes
4
replies
2.6k
views
Problem with Ensembl version identifiers after running DESeq2
DESEq2
Ensembl
identifiers
annotation
6.5 years ago by
Lila M
★ 1.2k
4
votes
3
replies
8.0k
views
how to remove Overrepresented sequences for paired end with cutadapt?
RNA-Seq
fastqc
cutadapt
trimming
paired-end
6.6 years ago by
Lila M
★ 1.2k
0
votes
1
reply
1.4k
views
is necessary to remove TruSeq index adapter with low percent and present in one read?
RNA-Seq
paired-end
adapters
quality control
6.6 years ago by
Lila M
★ 1.2k
8
votes
8
replies
6.8k
views
error when run tximport for salmon files
RNA-Seq
salmon
quantification
R error
txtimport
6.6 years ago by
Lila M
★ 1.2k
3
votes
2
replies
3.8k
views
which option is better for DESeq2 analysis: salmon or htseq-count?
RNA-Seq
Salmon
htseq-count
DE
updated 6.6 years ago by
Kristoffer Vitting-Seerup
★ 4.0k • written 6.6 years ago by
Lila M
★ 1.2k
3
votes
3
replies
2.5k
views
what is the best way annotate the genes in a data frame?
R
biomart
annotation
data frame
updated 6.7 years ago by
Kevin Blighe
87k • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 5 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
3
votes
6
replies
2.4k
views
Differential expressed genes in DESeq
DESeq
RNA
RNA-Seq
expression
updated 6.7 years ago by
Devon Ryan
104k • written 6.7 years ago by
Lila M
★ 1.2k
2
votes
11
replies
3.8k
views
Best way to compare expression values between two groups
comparation
p-value
R
updated 6.7 years ago by
theobroma22
★ 1.2k • written 6.7 years ago by
Lila M
★ 1.2k
1
vote
1
reply
1.5k
views
Error when Asm852v1 (S pombe) genome is installed in ngsplot
ngsplot
genome
ngs.plot.r
s.pmbe
updated 6.7 years ago by
Alastair Kerr
5.3k • written 7.2 years ago by
Lila M
★ 1.2k
5
votes
3
replies
4.4k
views
how to calculate the coverage over a specif coordinate
RNA-Seq
coverage
exon
6.8 years ago by
Lila M
★ 1.2k
5
votes
9
replies
3.3k
views
How can I check the direction of DNA replication?
replication
origin
transcription
6.8 years ago by
Lila M
★ 1.2k
6
votes
10
replies
2.9k
views
how to calling variants in RNAseq data from multiple samples?
RNA-Seq
GATK
VC
variant calling
updated 6.8 years ago by
Samuel Brady
▴ 330 • written 6.8 years ago by
Lila M
★ 1.2k
4
votes
7
replies
1.5k
views
How to check if specific mutations are or not enriched in a RNAseq data seq?
RNA-Seq
enriched
mutation
updated 6.8 years ago by
Istvan Albert
100k • written 6.8 years ago by
Lila M
★ 1.2k
2
votes
2
replies
1.9k
views
Is the heatmap matruix from vst expressed in fold change?
RNA-Seq
pheatmap
heatmap
vsd
fold change
updated 6.9 years ago by
Devon Ryan
104k • written 6.9 years ago by
Lila M
★ 1.2k
0
votes
2
replies
1.2k
views
dexseq_count.py: strandness of data from portal.gdc.cancer.gov
DEXseq
dexseq_count
TCGA
updated 6.9 years ago by
Istvan Albert
100k • written 6.9 years ago by
Lila M
★ 1.2k
1
vote
4
replies
3.4k
views
differential exon usage
RNA-Seq
exon
bam
updated 6.9 years ago by
Kristoffer Vitting-Seerup
★ 4.0k • written 7.0 years ago by
Lila M
★ 1.2k
0
votes
4
replies
1.3k
views
how to analyze the distribution over each gene in different conditions?
RNA-Seq
coverage
gene
6.9 years ago by
Lila M
★ 1.2k
1
vote
1
reply
2.6k
views
how to calculate coverage in bam file over a specific bed file
RNA-Seq
exon
coverage
multicov
bedtools
updated 6.9 years ago by
Devon Ryan
104k • written 6.9 years ago by
Lila M
★ 1.2k
2
votes
5
replies
1.6k
views
coverage for unique transcript and df process
R
data frame
coverage
updated 7.0 years ago by
Rashedul Islam
▴ 470 • written 7.0 years ago by
Lila M
★ 1.2k
1
vote
7
replies
3.2k
views
compare peaks in a gene list (coordinates)
ChIP-Seq
peaks
gene
bed
updated 7.1 years ago by
ivivek_ngs
★ 5.2k • written 7.1 years ago by
Lila M
★ 1.2k
1
vote
2
replies
2.8k
views
CpG islands density calculation
RNA-Seq
CpG
promoters
7.1 years ago by
Lila M
★ 1.2k
3
votes
18
replies
4.3k
views
how to identify TATA box in a gene list
TATA
homer
gene
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Lila M
★ 1.2k
3
votes
5
replies
1.1k
views
where to find a list of often mutated or lost regions in cancers
cance
gene
mutation
lost
database
7.1 years ago by
Lila M
★ 1.2k
1
vote
9
replies
2.0k
views
How to convert references ID list in UCSC reference list
ID
gene
name
UCSC
7.1 years ago by
Lila M
★ 1.2k
9
votes
7
replies
2.2k
views
s pombe non-coding regions annotation
ChIP-Seq
annotation
genome
ChIPseeker
non-coding
updated 7.2 years ago by
Guangchuang Yu
★ 2.6k • written 7.2 years ago by
Lila M
★ 1.2k
3
votes
2
replies
2.6k
views
warning trying to create a TxDB for S.pombe
ChIPseeker
pombe
TxDB
GRanges
Metadata
updated 7.2 years ago by
ddiez
★ 2.0k • written 7.2 years ago by
Lila M
★ 1.2k
10
votes
11
replies
1.7k
views
Lost in "if else" statement R
ChIP-Seq
R
if
else
loop
7.2 years ago by
Lila M
★ 1.2k
0
votes
2
replies
1.6k
views
select -500 from the TSS to +500 after the TES strand +/-
sequencing
strand
TSS
TES
coverage
updated 7.2 years ago by
Alex Reynolds
35k • written 7.2 years ago by
Lila M
★ 1.2k
5
votes
4
replies
1.9k
views
How to split a bed file according promoter window (-30 to 300bp)
ChIP-Seq
bed
deepTools
coverage
edit
7.2 years ago by
Lila M
★ 1.2k
2
votes
7
replies
9.5k
views
How to annotate TTS or TES
ChIP-Seq
TES
annotation
7.2 years ago by
Lila M
★ 1.2k
3
votes
6
replies
1.2k
views
select the highest value for the same gene
gene
ChIP-Seq
updated 7.2 years ago by
Pierre Lindenbaum
161k • written 7.2 years ago by
Lila M
★ 1.2k
3
votes
2
replies
1.6k
views
Select TSS to know if genes are differentially transcribed
ChIP-Seq
annotation
deepTools
R
ChIPseeker
updated 7.3 years ago by
Devon Ryan
104k • written 7.3 years ago by
Lila M
★ 1.2k
0
votes
2
replies
5.7k
views
Looking for a ClueGO (cytoscape) tutorial
GO
clueGO
Cytoscape
7.3 years ago by
Lila M
★ 1.2k
0
votes
4
replies
1.6k
views
How to start with bamsignals
ChIP-Seq
bam
bamsignal
bioconductor
R
updated 7.3 years ago by
GenoMax
142k • written 7.3 years ago by
Lila M
★ 1.2k
110 results • Page
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