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
682 results • Page
7 of 14
Sort: replies
Rank
Views
Votes
Replies
0
votes
2
replies
245
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
16 days ago by
dtnondorf
• 0
1
vote
2
replies
282
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
★ 7.2k • written 5 weeks ago by
Netanel
• 0
0
votes
2
replies
275
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
11 days ago by
sainavyav22
• 0
0
votes
2
replies
299
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
22 days ago by
Guille
• 0
0
votes
2
replies
192
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
4 days ago by
melissa.joubert
• 0
0
votes
2
replies
437
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
5 days ago by
David Langenberger
11k
1
vote
2
replies
230
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
11 days ago by
Assa Yeroslaviz
★ 1.8k
3
votes
2
replies
426
views
Extract protein sequence
fasta
alignment
blast
18 days ago by
anna
▴ 20
0
votes
2
replies
219
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 10 days ago by
Adam
▴ 30 • written 11 days ago by
Darya
• 0
5
votes
2
replies
443
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 23 days ago by
shalespringer
▴ 10 • written 3 months ago by
Phenylananin
▴ 20
0
votes
2
replies
281
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
24 days ago by
mropri
▴ 150
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 10 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
1
vote
2
replies
284
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 12 days ago by
Weiwen
• 0 • written 13 days ago by
MICOS
▴ 10
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
13 days ago by
bef1
• 0
0
votes
2
replies
867
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 24 days ago by
barslmn
★ 2.2k • written 2.8 years ago by
jhy
▴ 10
0
votes
2
replies
300
views
How are score_weights calculated in this code?
single-cell
8 days ago by
carolofharvest
▴ 40
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
2
votes
2
replies
251
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 20 days ago by
GenoMax
142k • written 20 days ago by
Winter
• 0
1
vote
2
replies
304
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
16 days ago by
eebloom
▴ 80
1
vote
2
replies
212
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
0
votes
2
replies
260
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
11 days ago by
Ahiad Chen Zion
• 0
0
votes
2
replies
289
views
Downloading older version of a tool
Alignment
tools
15 days ago by
Ruqaiya
• 0
0
votes
2
replies
235
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
9 days ago by
jain72744
▴ 10
0
votes
2
replies
349
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 23 days ago by
GenoMax
142k • written 24 days ago by
Begonia_pavonina
▴ 150
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 24 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
4
votes
2
replies
287
views
GRCh38.gmap file
gnomix
gmap
14 days ago by
lorena9132
▴ 10
2
votes
2
replies
187
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 2 days ago by
Ram
43k • written 3 days ago by
jsmith120f
• 0
1
vote
2
replies
195
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
11 days ago by
robert.flynn.21
• 0
0
votes
2
replies
279
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 8 days ago by
GenoMax
142k • written 15 days ago by
Ximena
• 0
7
votes
2
replies
330
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 25 days ago by
geneontologyhelp
▴ 400 • written 26 days ago by
catherine.teyssier
• 0
0
votes
2
replies
326
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 12 days ago by
Xiaofen
• 0 • written 12 days ago by
toddknutson
▴ 60
2
votes
2
replies
488
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 25 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
1
vote
2
replies
390
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
21 days ago by
Francesco
▴ 10
2
votes
2
replies
368
views
Association study using SNP data
Association
Allele
Parentage
SNP
13 days ago by
drajangirija
• 0
0
votes
2
replies
324
views
bam merging for archaic samples
samtools
bam
updated 27 days ago by
Ram
43k • written 28 days ago by
Matteo Ungaro
▴ 100
2
votes
2
replies
253
views
Raw counts using stringtie
stringtie
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ahmad.sajad4541
• 0
3
votes
2
replies
383
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 23 days ago by
dsull
★ 6.0k • written 23 days ago by
Aaliya
▴ 10
1
vote
2
replies
325
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
18 days ago by
Nafi
• 0
0
votes
2
replies
229
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
3 days ago by
Chen
• 0
1
vote
2
replies
184
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
0
votes
2
replies
200
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
20 days ago by
Lluís R.
★ 1.2k
1
vote
2
replies
231
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
2
replies
201
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 1 day ago by
LauferVA
4.2k • written 1 day ago by
ijarne
• 0
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
24 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
185
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
0
votes
2
replies
221
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
10 days ago by
Nicholas
• 0
0
votes
2
replies
756
views
homer not configured properly
Homer
makeTagDirectory
updated 16 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
2
votes
2
replies
254
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 10 days ago by
Michael
54k • written 10 days ago by
ashaneev07
▴ 20
2
votes
2
replies
318
views
p-value in CIBERSORT
CIBERSORT
p-value
18 days ago by
michelafrancesconi9
▴ 20
4
votes
2
replies
271
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 14 days ago by
Ram
43k • written 16 days ago by
carolofharvest
▴ 40
682 results • Page
7 of 14
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Recent Locations •
All
United States,
just now
Israel,
5 minutes ago
Vietnam,
8 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
8 minutes ago
Egypt,
8 minutes ago
Palau,
10 minutes ago
France,
14 minutes ago
Recent Awards •
All
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Popular Question
to
syedahamdani94
• 0
Popular Question
to
mohammadhassanj
▴ 260
Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Traffic: 1259 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