Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
399 results • Page
4 of 8
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
319
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 14 days ago by
GenoMax
142k • written 15 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
251
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
8 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
135
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 15 days ago by
Ram
43k • written 15 days ago by
Alexandros
• 0
0
votes
1
reply
185
views
unable to get feature count results
featureCounts
updated 15 days ago by
Ram
43k • written 15 days ago by
Ravita
• 0
0
votes
3
replies
310
views
KEGG Pathways
r
RNA-seq
updated 15 days ago by
Ram
43k • written 15 days ago by
Sudip
• 0
0
votes
0
replies
148
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
15 days ago by
Bine
▴ 60
1
vote
2
replies
238
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 15 days ago by
Ram
43k • written 15 days ago by
Ravita
• 0
3
votes
3
replies
259
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 1 day ago by
Ram
43k • written 15 days ago by
Adyasha
• 0
0
votes
0
replies
120
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
15 days ago by
fanglujing
▴ 60
0
votes
0
replies
144
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
15 days ago by
Jacob
• 0
0
votes
1
reply
193
views
Differential Accessibility
DiffBind
updated 15 days ago by
Ram
43k • written 15 days ago by
Shloka
• 0
0
votes
3
replies
313
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 15 days ago by
GenoMax
142k • written 15 days ago by
kim
• 0
3
votes
7
replies
392
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
16 days ago by
salias
• 0
0
votes
0
replies
136
views
Using limma in methylation EM-seq?
EM-seq
methylation
16 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
131
views
Synteny analysis
bacterial
synteny
genome
updated 16 days ago by
GenoMax
142k • written 16 days ago by
Namil
• 0
0
votes
4
replies
290
views
Genbank File Format
gbkformat
15 days ago by
alenew.am
• 0
0
votes
0
replies
260
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
16 days ago by
SSSJec
• 0
0
votes
3
replies
242
views
Software to separate reads from different individuals
software
development
nanopore
updated 15 days ago by
GenoMax
142k • written 16 days ago by
njornet
▴ 20
0
votes
2
replies
333
views
How to update R on ubuntu
installation
update
R
apt-get
16 days ago by
Bosberg
▴ 50
0
votes
0
replies
121
views
LEfSe
LEfSe
16 days ago by
benkosta
• 0
0
votes
0
replies
97
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
16 days ago by
Sara
▴ 30
0
votes
2
replies
187
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
16 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
114
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
0
votes
2
replies
231
views
What should I consider as FASTA for dataset?
PDB
FASTA
15 days ago by
Nafi
• 0
0
votes
0
replies
605
views
Differential accessibility using DiffBinf
diffbind
16 days ago by
Shloka
• 0
0
votes
0
replies
110
views
vg call vs vg surject
vg
variation
graphs
updated 16 days ago by
GenoMax
142k • written 16 days ago by
aliraza3119
• 0
0
votes
1
reply
236
views
Finding batch and outlayers
Pca
updated 16 days ago by
christopher medway
▴ 460 • written 16 days ago by
Tigran
• 0
2
votes
2
replies
236
views
PDB related issue
rcsb
pdb
updated 16 days ago by
noodle
▴ 580 • written 16 days ago by
Nafi
• 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 16 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
2
replies
273
views
Downloading full alignments from Pfam
pfam
10 days ago by
bef1
• 0
0
votes
0
replies
138
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 16 days ago by
dariober
14k • written 17 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
370
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Francesco
▴ 10
0
votes
0
replies
154
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
17 days ago by
tnminh89
▴ 10
0
votes
0
replies
157
views
Filter low express genes in microarray data
microarray
17 days ago by
Chris
▴ 280
0
votes
0
replies
585
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
18 days ago by
biocellbio
• 0
0
votes
0
replies
224
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
19 days ago by
HarperReed
• 0
1
vote
0
replies
174
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
19 days ago by
KABILAN
▴ 70
0
votes
0
replies
190
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 18 days ago by
Ram
43k • written 19 days ago by
SineWave
• 0
0
votes
0
replies
191
views
RNA-seq: full length gene
RNA-seq
updated 19 days ago by
Ram
43k • written 19 days ago by
Nargis
• 0
0
votes
0
replies
170
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
19 days ago by
turcoa1
• 0
0
votes
0
replies
183
views
Designing single-stable RNA molecules
structure
RNA
19 days ago by
Edna
• 0
0
votes
0
replies
194
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
19 days ago by
simplitia
▴ 130
1
vote
1
reply
264
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 19 days ago by
ATpoint
82k • written 19 days ago by
AaronJaime
• 0
0
votes
0
replies
180
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
1
vote
0
replies
192
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
20 days ago by
rohitsatyam102
▴ 860
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
20 days ago by
synat.keam
▴ 100
0
votes
1
reply
531
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 20 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
0
replies
174
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
20 days ago by
Aspire
▴ 330
0
votes
4
replies
411
views
Highest variable features in single cell data
single-cell
8 days ago by
carolofharvest
▴ 40
1
vote
3
replies
447
views
PCA plot
DESeq2
PCAplot
updated 16 days ago by
LauferVA
4.2k • written 20 days ago by
Aaliya
▴ 10
399 results • Page
4 of 8
Recent Votes
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Recent Locations •
All
Canada,
1 minute ago
Memphis, TN,
1 minute ago
United States,
3 minutes ago
United States,
3 minutes ago
United States,
3 minutes ago
United States,
6 minutes ago
United States,
6 minutes ago
Recent Awards •
All
Scholar
to
rpolicastro
13k
Popular Question
to
Amr
▴ 160
Popular Question
to
asalimih
▴ 60
Popular Question
to
nd48
▴ 20
Scholar
to
Trivas
★ 1.8k
Popular Question
to
biology_inform
▴ 50
Popular Question
to
Joe
21k
Recent Replies
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Traffic: 2577 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6