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Showing :
questions
3
votes
12
replies
490
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
23 days ago by
Lila M
★ 1.2k
0
votes
4
replies
299
views
Confirm if a genome position falls into a coding exon
exon
UCSC
coding
updated 4 weeks ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Lila M
★ 1.2k
1
vote
3
replies
361
views
'incomplete' intersect among two files
bedtools
bed
intersect
5 weeks ago by
Lila M
★ 1.2k
0
votes
1
reply
220
views
what is the best database for fusion genes ?
RNA-seq
fusion-genes
updated 9 weeks ago by
Yogi
▴ 70 • written 9 weeks ago by
Lila M
★ 1.2k
1
vote
13
replies
1.5k
views
What is the best way to retrieve gene name from variant mutation?
mutation
name
gene
variant
11 months ago by
Lila M
★ 1.2k
7
votes
8
replies
1.4k
views
retrieve amplicon sequences from fna file
amplicon
fna
primers
updated 16 months ago by
Juan MONROY-NIETO
▴ 30 • written 16 months ago by
Lila M
★ 1.2k
3
votes
4
replies
923
views
dealing with insertion in a data set
insertion
grep
dyplr
2.5 years ago by
Lila M
★ 1.2k
0
votes
0
replies
602
views
What is the codification in genestrand 1 and 2?
chipseeker
peakannotation
2.6 years ago by
Lila M
★ 1.2k
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping
coverage
DNA
genomic
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Lila M
★ 1.2k
9
votes
13
replies
3.6k
views
error when running bbduk
bbduk
error
updated 2.8 years ago by
h.mon
35k • written 2.8 years ago by
Lila M
★ 1.2k
3
votes
3
replies
2.4k
views
Nanopore tutorial for beginners
nanopore
updated 13 months ago by
Ram
43k • written 2.8 years ago by
Lila M
★ 1.2k
0
votes
3
replies
747
views
mapping with bfast killed when created index
bfast
mapping
index
updated 2.9 years ago by
JC
13k • written 2.9 years ago by
Lila M
★ 1.2k
0
votes
3
replies
679
views
very low number of reads aligned in bowtie (colourspace)
map
colourspace
bowtie
updated 2.9 years ago by
GenoMax
141k • written 2.9 years ago by
Lila M
★ 1.2k
7
votes
3
replies
4.1k
views
error bowtie2-align exited with value 134
fastq
bowtie2
updated 2.9 years ago by
ATpoint
82k • written 2.9 years ago by
Lila M
★ 1.2k
2
votes
4
replies
894
views
how to find homology in DNA regios
coordinates
homology
sequences
blast
2.9 years ago by
Lila M
★ 1.2k
0
votes
8
replies
1.4k
views
how to find homologous regions using genomic coordinates
homology
regions
genomic
updated 20 months ago by
Ram
43k • written 3.0 years ago by
Lila M
★ 1.2k
0
votes
0
replies
617
views
struggle to plot metagene profile with bed files
plot
profile
metagene
3.0 years ago by
Lila M
★ 1.2k
1
vote
8
replies
1.5k
views
how to select peaks at not transcribed genes
bedtools
transcribed
peaks
not_trasncribed
updated 3.0 years ago by
ATpoint
82k • written 3.0 years ago by
Lila M
★ 1.2k
0
votes
2
replies
1.3k
views
No annotation peaks when running homer
homer
peaks
tss
3.0 years ago by
Lila M
★ 1.2k
0
votes
1
reply
1.0k
views
Where to download raw counts (RNAseq) and breakpoints coordinates (cancer related) for testing?
RNAseq
cancer
updated 13 months ago by
Ram
43k • written 3.1 years ago by
Lila M
★ 1.2k
1
vote
0
replies
549
views
What is the best approach to correlate expression levels, mutated genes and clinical variables
RNA-Seq
correlation
mutation
3.1 years ago by
Lila M
★ 1.2k
0
votes
4
replies
574
views
best way to analyze a subset of DE genes
RNA-Seq
DESeq
expression
gene
3.1 years ago by
Lila M
★ 1.2k
4
votes
2
replies
5.8k
views
problems installing HTSeq
RNA-Seq
HTSeq
DEXSeq
updated 3.2 years ago by
Biostar
20 • written 7.0 years ago by
Lila M
★ 1.2k
1
vote
18
replies
1.2k
views
problem when create an expression matrix using a table
RNA-Seq
software error
R
expression
updated 3.2 years ago by
rpolicastro
13k • written 3.2 years ago by
Lila M
★ 1.2k
4
votes
2
replies
853
views
How to do a DESq analysis using a table with raw counts or normalized counts
R
RNA-Seq
DESeq
expersion
updated 3.2 years ago by
rpolicastro
13k • written 3.2 years ago by
Lila M
★ 1.2k
0
votes
2
replies
691
views
statitistical question: how can I say if there is a difference in the gene that fall inside/outside an especific region?
correlation
interdependence
gene distance
3.4 years ago by
Lila M
★ 1.2k
3
votes
2
replies
976
views
how to calculate distance from a single nucleotide position to a peak
ChIP-Seq
peak
distance
genome
updated 3.4 years ago by
Alex Reynolds
35k • written 3.4 years ago by
Lila M
★ 1.2k
4
votes
5
replies
1.7k
views
How to compare expression in gene list
expresion
statistic
R
updated 3.6 years ago by
Biostar
20 • written 7.1 years ago by
Lila M
★ 1.2k
15
votes
15
replies
6.0k
views
error while reading bigwig files in computeMatrix (deeptools)
deeptools
computeMatrix
bigwig
coverage
updated 3.0 years ago by
bli
• 0 • written 5.2 years ago by
Lila M
★ 1.2k
6
votes
8
replies
4.7k
views
How to smooth (ggplot2) 3 samples in the same plot
R
ggplot2
smooth
plot
ChIP-Seq
updated 4.2 years ago by
Biostar
20 • written 7.3 years ago by
Lila M
★ 1.2k
0
votes
0
replies
1.0k
views
How to identify confunders covariates in metagenomic analysis
metagenomic
confunding
multivariate
Maaslin
4.5 years ago by
Lila M
★ 1.2k
0
votes
7
replies
1.2k
views
re sampling for unbalanced samples
resamplig
unbalanced samples
4.6 years ago by
Lila M
★ 1.2k
0
votes
0
replies
1.3k
views
best way to do a boxplot for abundnace matrix (microbiome data)
abundance
microbiome
boxplot
ZIBR
4.7 years ago by
Lila M
★ 1.2k
0
votes
3
replies
917
views
How to analyze aCGH data in R?
aCGH
microarray
4.7 years ago by
Lila M
★ 1.2k
0
votes
1
reply
810
views
How to sumarize longotudinal data by patients and plot it?
longitudinal data
summary
plot
4.7 years ago by
Lila M
★ 1.2k
0
votes
0
replies
751
views
how to Dirichlet-multinomial mixture model over Bracken ssp abundance?
Bracken
metagenomics
microbiome
Dirichlet model
4.8 years ago by
Lila M
★ 1.2k
0
votes
3
replies
1.4k
views
how to plot an abundance table with ssp from metagenominc data
OTUs
metagenomic
microbiome
updated 4.8 years ago by
antonioggsousa
3.2k • written 4.8 years ago by
Lila M
★ 1.2k
2
votes
3
replies
826
views
where to download methylation data for colorectal cancer?
methylation
colorectal
public data
data
updated 4.8 years ago by
jared.andrews07
★ 16k • written 4.8 years ago by
Lila M
★ 1.2k
17
votes
18
replies
2.9k
views
How to deal with data set harmonization in R
R
coalesce
harmonization
data cleaning
updated 4.8 years ago by
Friederike
8.9k • written 4.8 years ago by
Lila M
★ 1.2k
5
votes
4
replies
1.2k
views
what is the best way to calculate significant differences in tss profiles?
coverage
differences
tss
updated 4.9 years ago by
Biostar
20 • written 5.1 years ago by
Lila M
★ 1.2k
3
votes
3
replies
1.1k
views
probles with loess normalization in affy
affy
microarray
loess
normalization
4.9 years ago by
Lila M
★ 1.2k
2
votes
1
reply
1.1k
views
How to analyze a ratio data set at different replication time point.
reliscan
ratio
repliseq
updated 4.9 years ago by
Biostar
20 • written 5.8 years ago by
Lila M
★ 1.2k
12
votes
7
replies
3.7k
views
how to solve this problem in bedtools genomecov?
bedtools
genomecov
mouse
updated 5.0 years ago by
ATpoint
82k • written 5.0 years ago by
Lila M
★ 1.2k
0
votes
0
replies
1.0k
views
How can I get the ID reference genes in GEO ?
ID
reference
GEO
gene ID
5.1 years ago by
Lila M
★ 1.2k
2
votes
2
replies
1.9k
views
error in prepare annotation script DEXseq
DEXseq
RNAseq
Ensamble
gencode
DEU
updated 5.1 years ago by
vida.t
• 0 • written 5.3 years ago by
Lila M
★ 1.2k
6
votes
4
replies
2.4k
views
How to calculate read depth for a specific gene list?
coverage
readdepth
interesct
5.2 years ago by
Lila M
★ 1.2k
2
votes
3
replies
1.4k
views
how to plot a TSS profile using an external quantification for Watson and Crick strand
ggplot
TSS
coverage
ratio
5.2 years ago by
Lila M
★ 1.2k
0
votes
0
replies
1.0k
views
How to deal with wig files separate bu watson and crick strand
wig
GROseq
TSSprofile
deepTools
5.3 years ago by
Lila M
★ 1.2k
16
votes
13
replies
2.8k
views
how to get correlation between the counts over each gene at the same timepoint (two replicates)
RNA-Seq
HTSeq
replication
correlation
updated 5.3 years ago by
Nicolas Rosewick
11k • written 5.3 years ago by
Lila M
★ 1.2k
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
109 results • Page
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