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116,008 results • Page
1 of 2321
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1
vote
1
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216
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
3 minutes ago by
Pierre Lindenbaum
160k
0
votes
1
reply
7
views
ONT direct RNA sequencing
gz
DRS
ONT
gunzip
gzip
updated 2 minutes ago by
dthorbur
★ 1.7k • written 9 minutes ago by
Karina
• 0
0
votes
0
replies
4
views
Flow Cytometry Data Analysis by Seurat
Seurat
10 minutes ago by
gdfsnkfns
• 0
0
votes
0
replies
12
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
38 minutes ago by
Lila M
★ 1.2k
0
votes
1
reply
22
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 41 minutes ago by
Ram
43k • written 1 hour ago by
Pumla
• 0
0
votes
1
reply
30
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 1 hour ago by
andrebolerbarros
• 0 • written 1 hour ago by
Christian
• 0
0
votes
1
reply
33
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 40 minutes ago by
Ram
43k • written 2 hours ago by
Mohamed Abderrahmane
• 0
0
votes
0
replies
19
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
2 hours ago by
Broccoli
• 0
0
votes
0
replies
26
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
2 hours ago by
blur
▴ 280
0
votes
0
replies
38
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
2 hours ago by
liuyibin2005
• 0
49
votes
29
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 2 hours ago by
ATpoint
81k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
33
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial
SPOTlight
transcriptomic
logFC
deconvolution
3 hours ago by
M'zelle
• 0
0
votes
3
replies
110
views
calculate mismatch rate from VCF file
rate
VCF
mismatch
updated 50 minutes ago by
Pierre Lindenbaum
160k • written 9 hours ago by
Dora
▴ 10
0
votes
0
replies
38
views
Downloading a list of all refseq assembly ids, including supressed assembliey
refseq
ncbi
assembly
3 hours ago by
Bertalan_Takacs
▴ 90
2
votes
3
replies
250
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 3 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
117
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
updated 5 hours ago by
kayah
• 0 • written 7 hours ago by
Nitin
• 0
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
0
votes
0
replies
50
views
In scRNA, How should I set QC standards?
scRNA
QC
6 hours ago by
mnx0723
• 0
0
votes
0
replies
43
views
Annotation of Complex genomes using NCBI Genome Workbench
annotation
Genome
MAKER
Workbench
7 hours ago by
SAsciences
• 0
0
votes
2
replies
219
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
8 hours ago by
lingxue
• 0
0
votes
0
replies
55
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
9 hours ago by
Chris
▴ 260
1
vote
10
replies
683
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 8 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
258
views
FDR and Bonferroni
FDR
Bonferroni
updated 9 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
0
votes
1
reply
466
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 12 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
69
views
doing some ontology enrichment analysis
GO
12 hours ago by
aleksk779
• 0
2
votes
1
reply
161
views
Choosing an FC Threshold
statistics
rna-seq
updated 12 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
102
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 15 hours ago by
Mensur Dlakic
★ 26k • written 21 hours ago by
Ricard
• 0
0
votes
2
replies
138
views
novel and know mir156 and mir172
a
updated 11 hours ago by
gayachit
▴ 200 • written 15 hours ago by
Fadmo
• 0
0
votes
1
reply
88
views
Update R in Posit Workbench
R
Posit
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Nitin
• 0
2
votes
8
replies
227
views
Piping samtools to R
R
NGS
bash
samtools
16 hours ago by
joe
▴ 470
8
votes
6
replies
374
views
Pangenome of plant
pangenome
plant
updated 18 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
170
views
vg call is time consuming
vg
18 hours ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 18 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
379
views
STAR aligner options
STAR
2 hours ago by
theophile
• 0
2
votes
3
replies
501
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 19 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
287
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 18 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
149
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
13 hours ago by
Ankit
▴ 500
0
votes
1
reply
97
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 18 hours ago by
Yogi
▴ 70 • written 20 hours ago by
Ronin
• 0
0
votes
0
replies
72
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 18 hours ago by
Ram
43k • written 20 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
74
views
Number of pathway result from GSVA
GSVA
20 hours ago by
Chris
▴ 260
0
votes
1
reply
110
views
How can I remove duplicate SNP?
plink
updated 21 hours ago by
iraun
6.2k • written 21 hours ago by
Zhennan
• 0
0
votes
1
reply
122
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 18 hours ago by
Ram
43k • written 21 hours ago by
Hajar
• 0
0
votes
0
replies
72
views
Creating a custom ontology for peptides
ontology
peptide
21 hours ago by
Mathew
• 0
0
votes
3
replies
191
views
convert cds to seurat object
R
monocle3
seurat
updated 40 minutes ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
73
views
GSEA number dimension of expression dataset
GSEA
21 hours ago by
edoardofilippi1998
• 0
0
votes
2
replies
209
views
Limma compare between 3 conditions vs 2 conditions
Limma
20 hours ago by
Chris
▴ 260
0
votes
0
replies
80
views
single cell data integration approach
comparison
integration
pairwise
singlecell
23 hours ago by
Jay
• 0
0
votes
3
replies
207
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
21 hours ago by
sarahmanderni
▴ 100
1
vote
1
reply
199
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 1 day ago by
GenoMax
140k • written 1 day ago by
JH
• 0
0
votes
2
replies
147
views
Error with goodSamplesGenes()
R
WGCNA
18 hours ago by
bioinfo_enthusiast
• 0
116,008 results • Page
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Recent Votes
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
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Recent Replies
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
Comment: Coverage observed in introns in the Knockdown genes but not in knockout genes
by
rohitsatyam102
▴ 840
As per the image below obtained by Running RNASeQC the intronic reds aren't that much (See the knockdown samples enclosed in the Red box) (…
Comment: Parsing fasta file by coordinates
by
Joe
21k
Am I understanding this correctly, that what you are looking for is any sequence where *any part* of the coord range overlaps with *any oth…
Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
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