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121,478 results • Page
1 of 2430
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Votes
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0
votes
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replies
14
views
How do I combine or integrate my VDJ data for TCR and BCR with seurat object?
VDJ
scRepertoire
Seurat
updated 44 minutes ago by
GenoMax
152k • written 1 hour ago by
Jaber
▴ 30
0
votes
0
replies
21
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
1 hour ago by
abedkurdi10
▴ 190
0
votes
1
reply
163
views
DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
updated 2 hours ago by
yura.grabovska
▴ 780 • written 2 days ago by
Picasa
▴ 680
1
vote
3
replies
246
views
RNA-seq: TPM batch effect correction
TPM
Combat
RNA-seq
updated 1 day ago by
rfran010
★ 1.6k • written 2 days ago by
Samuel
▴ 10
1
vote
3
replies
200
views
Error running pbrun fq2bam: No space left on device
disk
space
updated 6 hours ago by
DBScan
▴ 490 • written 2 days ago by
Ritu
• 0
2
votes
5
replies
232
views
Need help using ExpansionHunter
ExpansionHunter
updated 3 hours ago by
GenoMax
152k • written 1 day ago by
brianhill_nc
• 0
2
votes
3
replies
1.6k
views
How to find the annotation file for GPL16956 platform of Arraystar human lncRNA microarray V3 (Probe Name Version)?
annotation
lncRNA
microarray
probe
updated 11 hours ago by
GenoMax
152k • written 5.1 years ago by
daphneolivia39
▴ 20
840
votes
170
replies
181k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
5
replies
201
views
Statistics for bins
data
shotgun
updated 18 hours ago by
GenoMax
152k • written 1 day ago by
shevch2009
▴ 20
3
votes
4
replies
282
views
twist exome panel analysis
twist
exome
updated 20 hours ago by
GenoMax
152k • written 3 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
107
views
Run hifiasm without error correction module?
hifiasm
assembly
wgs
nanopore
genomics
updated 1 day ago by
shelkmike
★ 1.6k • written 1 day ago by
Mark
▴ 60
1
vote
1
reply
140
views
PhageTerm Galaxy
error
phageterm
genomics
updated 1 day ago by
GenoMax
152k • written 2 days ago by
NIkita
• 0
0
votes
0
replies
108
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
2 days ago by
Chijioke
• 0
1
vote
1
reply
142
views
Demultiplexing of snAtcSeq data using demuxlet gives an empty output
genotype
demuxlet
scatacseq
demultiplexing
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Bioiris
▴ 10
0
votes
1
reply
414
views
PbJelly Resume
Gap-filling
PacBio
PbJelly
written 12 months ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
100
views
How do I figure out which chain a ligand is bound to using rcsb-api?
rcsb
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Priyal
▴ 10
1
vote
2
replies
253
views
Deseq2
PyDeseq2
Deseq2
updated 2 days ago by
GenoMax
152k • written 3 days ago by
sk_24
▴ 10
0
votes
0
replies
134
views
News:
In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
ChIPSeq
BisulfiteSeq
ATACSeq
workshop
3 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
151
views
News:
Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
3 days ago by
Wei
• 0
2
votes
1
reply
352
views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
CicRNA-GEO
updated 3 days ago by
rfran010
★ 1.6k • written 3 days ago by
ParastooA
▴ 20
0
votes
4
replies
310
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 2 days ago by
GenoMax
152k • written 3 days ago by
k.lagan
• 0
1
vote
6
replies
350
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
2 days ago by
alejandro.mejiam1
▴ 20
0
votes
0
replies
161
views
low variant sites similarity between linear reference and vg call path
call
vg
updated 3 days ago by
GenoMax
152k • written 3 days ago by
PolenP
• 0
0
votes
0
replies
170
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization
DEG
KEGG
R
pathway
3 days ago by
txema.heredia
▴ 240
0
votes
5
replies
341
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
4 hours ago by
María José
▴ 10
4
votes
1
reply
542
views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
updated 3 days ago by
ATpoint
88k • written 4 days ago by
totoroGirl
• 0
0
votes
1
reply
251
views
Interactive UMAP scanpy
UMAP
scanpy
interactive
updated 4 days ago by
antonioggsousa
3.4k • written 4 days ago by
npont
▴ 10
9
votes
5
replies
353
views
Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
Batchcorrection
VOOM
DEGanalysis
Limma
bulkRNA
updated 3 days ago by
i.sudbery
21k • written 4 days ago by
Sumeet
▴ 10
7
votes
5
replies
517
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
6 days ago by
SomeOne
▴ 240
0
votes
0
replies
159
views
News:
online course: Sex Chromosome Evolution - 6–10 October 2025
SexChromosome
Evolution
Genomics
4 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
168
views
GSEA of sugarcane
GSEA
4 days ago by
analyst
▴ 70
4
votes
6
replies
620
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
updated 3 days ago by
txema.heredia
▴ 240 • written 9 days ago by
Cristina
• 0
1
vote
12
replies
610
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
4 days ago by
HarperReed
• 0
1
vote
2
replies
284
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN
calling
IgG
peak
4 days ago by
Basti
★ 2.1k
7
votes
3
replies
412
views
custom BED to UCSC genome browser
browser
ucsc
ucsc-genome-browser
genome
methylation
bed
5 days ago by
npont
▴ 10
1
vote
2
replies
279
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
4 days ago by
德水
• 0
0
votes
1
reply
253
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq
deeptools
updated 5 days ago by
GenoMax
152k • written 5 days ago by
Qilin
• 0
0
votes
0
replies
205
views
check vsiRNA expression of mosquito (smallRNA seq data)
seq
expression
data
smallRNA
mosquito
vsiRNA
5 days ago by
ZuelTech
• 0
0
votes
11
replies
554
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
5 days ago by
Jon
• 0
2
votes
1
reply
238
views
Quantification for small RNAseq data
quantification
seq
data
smallRNA
updated 5 days ago by
rfran010
★ 1.6k • written 5 days ago by
ZuelTech
• 0
6
votes
4
replies
376
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
3 days ago by
Anjan
▴ 840
0
votes
2
replies
496
views
Scvi - Integration
integration
singlecell
scvi
4 days ago by
t.foskolos
• 0
7
votes
3
replies
394
views
Bootstrapping in RNA-seq
bootstrapping
RNAseq
updated 5 days ago by
rfran010
★ 1.6k • written 6 days ago by
littlebioinformatician
• 0
1
vote
2
replies
379
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
3 days ago by
Shakunthala Natarajan
• 0
1
vote
0
replies
547
views
Job:
Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
Sweden
SciLifeLab
Genomics
Uppsala
Proteomics
4 days ago by
Matthias Zepper
5.1k
2
votes
2
replies
304
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
6 days ago by
joe_genome
▴ 60
0
votes
0
replies
230
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
6 days ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
339
views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded
STAR
RNAseq
antisense
sense
updated 6 days ago by
rfran010
★ 1.6k • written 7 days ago by
yampolsk
▴ 10
0
votes
1
reply
323
views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling.
rnaseq
gatk
updated 6 days ago by
rfran010
★ 1.6k • written 7 days ago by
iamsmor
• 0
0
votes
0
replies
240
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
6 days ago by
yu
• 0
121,478 results • Page
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Answer: Error running pbrun fq2bam: No space left on device
GW: fast genome browser and variant exploration tool
Answer: Calculation of allele frequency using 1000 genome project as reference panel
Genome Assembly Review Papers
Table Of Contents To All Review Paper Compilations On Biostar
Genotype And Snp Calling Review Papers
Integrating VDJ sequencing data with Seurat
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Answer: DGE analysis in Seurat using paired samples per donor ?
by
yura.grabovska
▴ 780
If all you're interested in doing is doing tumour vs non-tumour from 5 cases then why not create a pseudobulk and just run normal DESeq2 on…
Answer: RNA-seq: TPM batch effect correction
by
i.sudbery
21k
I'm with @rfran010 here. If you're goal is to compare genes within samples, then since all measurements from within a sample come from the …
Comment: Need help using ExpansionHunter
by
GenoMax
152k
> Should I use my Crai or FastQ files as a reference file? Can I produce a reference file from those? No you can't do that. You will have …
Comment: MACS3 Parameter adjustments
by
María José
▴ 10
Thanks, I have used the options `--keep-dup = all` and `--keep-dup = 1`, without previously performing a filter process with samtools or P…
Answer: Error running pbrun fq2bam: No space left on device
by
DBScan
▴ 490
Did you specify the temporary directory? If it's not specified, the directory points to you current directory where maybe a quota is in pla…
Comment: Error running pbrun fq2bam: No space left on device
by
Ritu
• 0
I know about this but why this is happening with 25 GB1000 genome project dataset not for 48 GB NCBI fastq dataset.
Comment: Need help using ExpansionHunter
by
brianhill_nc
• 0
Thanks for helping me. I did get the Warp terminal ExpansionHunter command line to run and produce an output file. But I believe the refe…
Comment: How to find the annotation file for GPL16956 platform of Arraystar human lncRNA
by
GenoMax
152k
You can find the probe sequences in this table: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL16956&id=25054&db=GeoDb_blo…
Comment: How to find the annotation file for GPL16956 platform of Arraystar human lncRNA
by
Ahmed Jaber
• 0
please, Did you find any answer for this question as i am stuck in it now!!
Comment: Statistics for bins
by
GenoMax
152k
k127_5845587 2388 k127_1599072 5710 k127_4786624 15259 That is the name of the fasta header followed by length of…
Comment: Statistics for bins
by
shevch2009
▴ 20
It seems I have found a solution, but without an individual lengths of all scaffolds/contigs per bin.... seqkit stats -a -T /reassembled…
Comment: Statistics for bins
by
shevch2009
▴ 20
The next code didn't provides what I need seqkit fx2tab --length --name --header-line foo.fasta I got strange table k127_58455…
Comment: twist exome panel analysis
by
GenoMax
152k
With the exception of one sample looks like others have adequate coverage.
Comment: Statistics for bins
by
shevch2009
▴ 20
Thanks GenoMax, I will try those tools.
Comment: twist exome panel analysis
by
1769mkc
★ 1.3k
"For exome sequencing experiments, the coverage standard for confidence in an experiment is 20x – that is, 20 sequenced fragments align wit…
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