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121,476 results • Page
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DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
updated 44 minutes ago by
yura.grabovska
▴ 780 • written 2 days ago by
Picasa
▴ 680
1
vote
3
replies
236
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
0
votes
3
replies
192
views
Error running pbrun fq2bam: No space left on device
disk
space
updated 4 hours ago by
DBScan
▴ 480 • written 2 days ago by
Ritu
• 0
2
votes
5
replies
219
views
Need help using ExpansionHunter
ExpansionHunter
updated 2 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 9 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
197
views
Statistics for bins
data
shotgun
updated 17 hours ago by
GenoMax
152k • written 23 hours ago by
shevch2009
▴ 20
3
votes
4
replies
277
views
twist exome panel analysis
twist
exome
updated 19 hours ago by
GenoMax
152k • written 3 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
106
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
139
views
PhageTerm Galaxy
error
phageterm
genomics
updated 1 day ago by
GenoMax
152k • written 1 day ago by
NIkita
• 0
0
votes
0
replies
107
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
1 day ago by
Chijioke
• 0
1
vote
1
reply
140
views
Demultiplexing of snAtcSeq data using demuxlet gives an empty output
genotype
demuxlet
scatacseq
demultiplexing
updated 1 day ago by
GenoMax
152k • written 2 days ago by
Bioiris
▴ 10
0
votes
1
reply
413
views
PbJelly Resume
Gap-filling
PacBio
PbJelly
written 12 months ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
99
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
250
views
Deseq2
PyDeseq2
Deseq2
updated 2 days ago by
GenoMax
152k • written 3 days ago by
sk_24
▴ 10
0
votes
0
replies
133
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
148
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
350
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
308
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
349
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
2 days ago by
alejandro.mejiam1
▴ 20
0
votes
0
replies
160
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
169
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
332
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
2 hours ago by
María José
▴ 10
4
votes
1
reply
539
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
248
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
349
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
516
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
5 days ago by
SomeOne
▴ 240
0
votes
0
replies
157
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
167
views
GSEA of sugarcane
GSEA
4 days ago by
analyst
▴ 70
4
votes
6
replies
615
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
605
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
4 days ago by
HarperReed
• 0
1
vote
2
replies
282
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
411
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
276
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
4 days ago by
德水
• 0
0
votes
1
reply
252
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
204
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
552
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
5 days ago by
Jon
• 0
2
votes
1
reply
237
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
373
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
3 days ago by
Anjan
▴ 840
0
votes
2
replies
495
views
Scvi - Integration
integration
singlecell
scvi
4 days ago by
t.foskolos
• 0
7
votes
3
replies
393
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
377
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
3 days ago by
Shakunthala Natarajan
• 0
1
vote
0
replies
542
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
302
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
6 days ago by
joe_genome
▴ 60
0
votes
0
replies
229
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
6 days ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
338
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
322
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
239
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
6 days ago by
yu
• 0
5
votes
6
replies
640
views
Venn Diagram
VennDiagram
updated 5 days ago by
lieven.sterck
15k • written 9 days ago by
Nasim Gandomdoust
• 0
0
votes
1
reply
292
views
PhageTerm error
phage
genome
phageterm
assamble
updated 6 days ago by
GenoMax
152k • written 6 days ago by
NIkita
• 0
121,476 results • Page
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Recent Votes
GW: fast genome browser and variant exploration tool
Answer: Calculation of allele frequency using 1000 genome project as reference panel
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Integrating VDJ sequencing data with Seurat
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
▴ 480
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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