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190 results • Page
3 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
6
replies
305
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
2 days ago by
Sd
• 0
0
votes
2
replies
175
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
3 days ago by
sainavyav22
• 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
310
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
3
votes
9
replies
419
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Κοσμάς
• 0
0
votes
0
replies
107
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
191
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
c_u
▴ 520
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
0
replies
197
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
196
views
from row count to tpm
tpm
row-count
normalization
3 days ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
266
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
2
votes
3
replies
318
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 hours ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
0
votes
1
reply
130
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
6
replies
226
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 48 minutes ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
3
votes
3
replies
218
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Mariana
▴ 10
0
votes
1
reply
124
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 4 days ago by
ATpoint
82k • written 4 days ago by
enanoide
• 0
0
votes
0
replies
85
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
4 days ago by
manaswwm
▴ 490
3
votes
3
replies
716
views
KissDE and batch effect
kissDE
kissplice
4 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
75
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
1 day ago by
Kevin Blighe
87k
0
votes
0
replies
82
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
4 days ago by
feather-W
• 0
2
votes
4
replies
262
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
2 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
81
views
Annotating single cell data automatically
cell
annotation
single
4 days ago by
Gerard
• 0
0
votes
0
replies
82
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
125
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
296
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
2 days ago by
HyperEvo
• 0
0
votes
1
reply
149
views
RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sh
• 0
0
votes
2
replies
191
views
Result of running of p3_in.pl
primer3
updated 4 days ago by
GenoMax
141k • written 4 days ago by
nasri
• 0
0
votes
1
reply
131
views
FAM FILE
file
Fam
4 days ago by
Eleonora
• 0
0
votes
0
replies
73
views
Imputation advice
imputation
4 days ago by
kl
▴ 10
3
votes
5
replies
263
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 4 days ago by
GenoMax
141k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
90
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
4 days ago by
Enrique
• 0
3
votes
5
replies
544
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
4 days ago by
n_navy
• 0
0
votes
0
replies
73
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
4 days ago by
sativus
▴ 20
6
votes
3
replies
179
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
0
votes
1
reply
174
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
Ayush
• 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
4 days ago by
Biostars2200
• 0
1
vote
5
replies
318
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
3 days ago by
anasjamshed
▴ 120
0
votes
0
replies
125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
Atul K.
• 0
3
votes
2
replies
271
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
4 days ago by
kristiewyleung
• 0
2
votes
5
replies
450
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 5 days ago by
Lipika
• 0
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
5 days ago by
rthapa
▴ 90
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
5 days ago by
Mamatha Y S
• 0
0
votes
0
replies
130
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 5 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
523
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 days ago by
ATpoint
82k • written 6 days ago by
rheab1230
▴ 140
0
votes
2
replies
260
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
190 results • Page
3 of 4
Recent Votes
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
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