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 : all time
all time
today
this week
this month
this year
121,981 results • Page
246 of 2440
Sort: Rank
Rank
Views
Votes
Replies
3
votes
6
replies
2.1k
views
Obtain counts for specific genes with ChIP-seq data without peak calling
ChIP-seq
2.3 years ago by
marinamrbiotech
▴ 10
2
votes
3
replies
1.1k
views
Convert Bam to Fastq
Fastq
Bam
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
وفاء
• 0
0
votes
1
reply
1.2k
views
Variant calling analysis on phased assembly
variant-calling
bam
pbsv
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
pablo
▴ 350
2
votes
7
replies
1.5k
views
Samtools merge bam issue with header tags
SamTools
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
sam
▴ 30
0
votes
2
replies
1.4k
views
Exception in thread "main" java.io.EOFException: Unexpected end of ZLIB input stream
trimmomatic
2.3 years ago by
Ahmed
▴ 10
0
votes
1
reply
1.1k
views
SnpEff output VCF in `.gz` format
snpeff
updated 2.3 years ago by
Pierre Lindenbaum
166k • written 2.3 years ago by
ttom
▴ 230
0
votes
0
replies
492
views
Query regarding DNA Methylation Bisulfite Sequencing data analysis
methylkit
DNA
methylation
2.3 years ago by
Pankaj
• 0
0
votes
1
reply
990
views
demultiplex bcl files from 10X genomics and generate fastq file for each sample separately
scRNAseq
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
Sara
▴ 280
0
votes
0
replies
751
views
Job:
Postdoc in Proteomics and Cell Signalling
cell
ubiquitylation
proteomics
signalling
phosphorylation
2.3 years ago by
info
▴ 80
3
votes
4
replies
2.0k
views
gff3 to gtf
gtf
gff3
2.3 years ago by
bestone
▴ 30
0
votes
0
replies
1.2k
views
News:
Hands-On NGS Data Analysis Courses 2023
RNA-seq
DNA-seq
Workshop
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
David Langenberger
11k
0
votes
0
replies
625
views
Correct 18S data file to assign taxonomy
dada2
R
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Bioinfo
▴ 20
7
votes
8
replies
4.7k
views
Forum:
Would solving many Rosalind problems show your ability for this field in job-wise?
rosalind
career
2.3 years ago by
K
• 0
2
votes
1
reply
749
views
Taxonomic binning of assembly from WGS
Binning
updated 2.3 years ago by
Mensur Dlakic
★ 30k • written 2.3 years ago by
Dee
• 0
2
votes
1
reply
1.0k
views
Choosing the right batch effect control algorithm for bulk RNA-seq data meta-analysis
PEER
SVA
RUV
RNA-seq
updated 2.3 years ago by
Papyrus
★ 3.1k • written 2.3 years ago by
LauferVA
4.8k
0
votes
4
replies
1.3k
views
Other independent methods or ways to confirm potential candidate genes observed through variant calling and homozygosity analysis
candidate-genes
plink
Variant-calling
Homozygosity-analysis
2.3 years ago by
somatohadidas
• 0
1
vote
2
replies
1.4k
views
How to choose the important clusters for RNAseq data of different groups for downstream analysis/annotation
RNA-seq
cluster
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
alwayshope
▴ 40
1
vote
3
replies
1.2k
views
Heatmap
Log2FoldChange
Heatmap
2.3 years ago by
smanzano250800
• 0
0
votes
5
replies
1.3k
views
Using IMmuno-PREdictive Score (IMPRES)
scaling
TPM
cancer
normalization
r
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
AlexStar
▴ 200
0
votes
0
replies
492
views
Are optimal narrowPeak datasets for histone marks available on the ENCODE website?
Histones
ChIP-seq
ENCODE
2.3 years ago by
aaronlogsdon2001
• 0
2
votes
8
replies
2.7k
views
Providing multiple read files to Salmon
salmon
rna-seq
updated 23 months ago by
Lada
▴ 40 • written 2.3 years ago by
ExtentHonest56
▴ 30
0
votes
0
replies
706
views
Correlation of gene expression in Spatial Transcriptomics (ELI5)
Statistics
Seurat
Single-Cell
Spatial-Transcriptomics
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
ivingan
• 0
8
votes
3
replies
1.7k
views
extreme high log2FoldChange in DESeq2 result
log2FoldChange
DESeq2
RNA-seq
DGEA
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
Sara
▴ 40
0
votes
0
replies
478
views
Reference Panel for Copy Number Analysis Based on Clinical Target Capture Sequencing
copynumber
target-capture
2.3 years ago by
Noushin N
▴ 620
1
vote
2
replies
883
views
DEG analysis of RNAseq TCGA data AFTER batch effect removal !!!
TCGA
Batch-effect
DEseq2
Swamp
2.3 years ago by
mohammad
• 0
1
vote
2
replies
1.8k
views
conda error
conda
2.3 years ago by
bestone
▴ 30
2
votes
2
replies
1.1k
views
fastq.gz how to split.
fastq.gz
split
2.3 years ago by
Andy
▴ 120
11
votes
6
replies
2.9k
views
"nextflow pull nf-core/sarek --help" returned "connection failed" ?
nextflow
sarek
nf-core
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Glt
• 0
0
votes
3
replies
1.5k
views
how to costum the color palette for ggplot2
ggplots
2.3 years ago by
Qianjiang(QJ) Hu
▴ 10
2
votes
1
reply
914
views
Gene prediction in the era of long read sequencing data and many reference genomes
gene-prediction
2.3 years ago by
William
★ 5.4k
0
votes
1
reply
2.1k
views
GOATOOLS to perform Gene ontology enrichment analyses in Python in a non model organism.
Python
RNA-seq
Trascriptomics
Gene-Ontology
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
Sbrillo
▴ 10
0
votes
0
replies
1.0k
views
All cells have the same value (0) of gene1.
featureplot
singlecellRNA
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
archanaverma433
▴ 10
5
votes
5
replies
1.7k
views
Normalized counts bulk RNA-seq to DEGs
RNA-seq
updated 2.3 years ago by
LauferVA
4.8k • written 2.3 years ago by
t.ru
▴ 20
0
votes
0
replies
543
views
Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals
GATK
SNPs
2.3 years ago by
mohsamir2016
▴ 30
4
votes
4
replies
2.5k
views
SRA: is it possible to download files in the original format?
FASTQ
SRA
updated 14 months ago by
GenoMax
154k • written 2.3 years ago by
markgodek
▴ 50
0
votes
0
replies
646
views
Running GCTA/GSMR and getting an error for .fam file
PLINK
GSMR
GCTA
.fam
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
999.me
• 0
0
votes
3
replies
1.3k
views
Need help using Biopython
Biopython
Anaconda
Microsoft
visual-studio
updated 2.3 years ago by
Jonathan Lefebre
▴ 70 • written 2.3 years ago by
Joseph
• 0
2
votes
2
replies
805
views
conda env error?
conda
env
updated 2.3 years ago by
biofalconch
★ 1.3k • written 2.3 years ago by
bestone
▴ 30
1
vote
2
replies
1.5k
views
Snpeff run with downloaded genome database
snpeff
updated 2.3 years ago by
estpallag
▴ 10 • written 2.3 years ago by
ttom
▴ 230
0
votes
0
replies
512
views
How to find the correlation between two genes and their separate overall survival outcome?
gene-expression
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
hind.sami
• 0
0
votes
0
replies
649
views
How to interpret reference and alternative alleles from raw plink data?
plink
GWAS
LD
genomics
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
genqs
• 0
3
votes
2
replies
3.8k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein
parallel
hmmer
hmm
bash
updated 2.3 years ago by
lieven.sterck
16k • written 4.2 years ago by
O.rka
▴ 750
0
votes
1
reply
567
views
SBS Mutational Signatures aetiology
signature
Mutational
2.3 years ago by
Z_Wael
▴ 10
2
votes
1
reply
1.3k
views
Seurat
RunPCA
RunUMAP
2.3 years ago by
friguiahlem8
▴ 30
7
votes
5
replies
2.7k
views
What are your preferred programs for processing DNA long reads? (de novo assembly)
assembly
de-novo
long-read
2.3 years ago by
ExtentHonest56
▴ 30
2
votes
3
replies
1.7k
views
Method to detect genome doubling
CNV
genome doubling
updated 17 months ago by
LauferVA
4.8k • written 5.9 years ago by
CY
▴ 750
0
votes
1
reply
766
views
Data normalization and analysis
SARS-Cov-2
drug
linux
updated 21 months ago by
Ram
45k • written 2.3 years ago by
Adyasha
• 0
0
votes
4
replies
1.2k
views
Post mapping extract query sequence mapped to each gene feature
samtools
seqkit
updated 2.3 years ago by
GenoMax
154k • written 2.3 years ago by
L_bioinfo
• 0
0
votes
0
replies
1.3k
views
Job:
Computational Scientist/ Spatial Biology - Frederick National Lab for Cancer Research
spatial-biology
updated 2.3 years ago by
Ram
45k • written 2.3 years ago by
lauri.rimorin
• 0
0
votes
0
replies
381
views
How to successfully upload gene expression data in DyNetViewer
DyNetViewer
2.3 years ago by
2997378860
• 0
121,981 results • Page
246 of 2440
Recent Votes
Answer: Dorado in PowerShell on Windows
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: When to merge RNA-seq files with multiple sequencing lanes
Answer: When to merge RNA-seq files with multiple sequencing lanes
Answer: Deeptools PlotProfile
Comment: GUI commercial software for 10x single cell gene expression analysis
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Recent Locations •
All
UCLA,
1 minute ago
Tunisia,
18 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
25 minutes ago
Türkiye,
31 minutes ago
Finland,
33 minutes ago
United States,
33 minutes ago
United States,
34 minutes ago
Recent Awards •
All
Popular Question
to
Info-rggs
▴ 20
Popular Question
to
sbissi102
▴ 10
Popular Question
to
AellSidious
• 0
Scholar
to
DdogBoss
▴ 20
Teacher
to
LChart
5.1k
Popular Question
to
Apprentice
▴ 190
Scholar
to
yura.grabovska
▴ 830
Recent Replies
Comment: Dorado in PowerShell on Windows
by
sbissi102
▴ 10
Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
by
DdogBoss
▴ 20
Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
Answer: GUI commercial software for 10x single cell gene expression analysis
by
Nicole
• 0
Many researchers use the CLC Genomics Workbench and Ingenuity Pathway Analysis. CLC can be used to do secondary analysis for your dataset a…
Comment: Diffbind or DESEQ2 Chipseq data
by
Irene
• 0
For example, in this image, the red area represents the differentially acetylated region returned by DiffBind. The green area is a promoter…
Comment: GUI commercial software for 10x single cell gene expression analysis
by
GenoMax
154k
Interesting pricing model : https://www.nygen.io/pricing Depending on user needs could be used (or certainly tested) for free. And this is …
Answer: Dorado in PowerShell on Windows
by
GenoMax
154k
> yet I received 96 fastq files in demux_out that corresponded to the 96 barcodes. Additionally, I'm unsure if I should re-trim the fastq f…
Comment: Dorado in PowerShell on Windows
by
jared.andrews07
★ 19k
If you're using WSL, PowerShell has nothing to do with this. It also sounds like a better question for your sequencing facility/provider ra…
Answer: GUI commercial software for 10x single cell gene expression analysis
by
Arup Ghosh
3.4k
Except for GSEA, the app from Nygen can perform most of the analysis using a tool similar to Scanpy. Docs: https://www.nygen.io/knowledge-…
Comment: Quantification using salmon in alignment-based mode after minimap2 run
by
Rob
7.1k
Hi Assa, Unless you have an additional use for the intermediate BAM file, I would recommend the read-based quantification mode. It is s…
Comment: GUI commercial software for 10x single cell gene expression analysis
by
GenoMax
154k
> Single-cell analysis is a complex topic and it's easy to make wonky conclusions from wonky analysis. Let us set aside a discussion of op…
Comment: How much coverage is needed for high-quality phylogenetic and admixture analyses
by
colindaven
8.0k
How much short read coverage do other studies have which you want to replicate? Are those studies using whole genomes creating using long r…
Comment: GUI commercial software for 10x single cell gene expression analysis
by
firestar
★ 1.7k
They have 10X cellranger output (ie; counts). They want to perform the standard sort of Seurat/Scanpy analyses: QC, filtering, integration,…
Comment: GUI commercial software for 10x single cell gene expression analysis
by
yura.grabovska
▴ 830
Can you provide more information on the use case? If they want to generate data for a publication I would argue that the majority of the GU…
Comment: tximport error (medianLengthOverIsoform)
by
LGG
• 0
I believe using `ignoreTxVersion = TRUE` is supposed to take care of that
Comment: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
tungsega
▴ 10
Just a very brief summary of the results using the latest versions of minimap2 and winnowmap (by `samtools stats`). It seems that winnowma…
Traffic: 2957 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