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121,501 results • Page
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0
votes
0
replies
40
views
PAML output
PAML
Codeml
Selection
3 hours ago by
Morjina
• 0
0
votes
0
replies
43
views
how to produce your own Nx plot
R
contiguity
plot
Nx
3 hours ago by
Matteo Ungaro
▴ 120
0
votes
1
reply
81
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree
phylogenetic
blast
updated 6 hours ago by
Mensur Dlakic
★ 29k • written 6 hours ago by
triplee0305
▴ 20
0
votes
0
replies
45
views
News:
Online course - Environmental Metagenomics - 13-17 October
Illumina
MAGs
Nanopore
Metagenomics
7 hours ago by
Physalia-courses
★ 2.6k
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
2
replies
131
views
Deg Difference in Deseq2
Deg
updated 8 hours ago by
swbarnes2
15k • written 12 hours ago by
j.k.owaresat
• 0
0
votes
0
replies
75
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est
Trinity
RNAseq
Trinotate
updated 9 hours ago by
GenoMax
152k • written 11 hours ago by
ofarinas621
• 0
0
votes
2
replies
108
views
MultiQC report - unique reads from sequence counts
fastQC
unique
reads
multiQC
updated 2 hours ago by
rfran010
★ 1.6k • written 11 hours ago by
Rozita
▴ 40
1
vote
3
replies
161
views
NCBI Reference Genomes
genomes
ncbi
updated 13 hours ago by
GenoMax
152k • written 17 hours ago by
anna
▴ 70
0
votes
0
replies
75
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon
gene_panel
haplotypecaller
variant_calling
gatk
14 hours ago by
Sofya
• 0
0
votes
0
replies
112
views
Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger multi with Combined Human-Mouse Reference
gem_classification
10x
cellranger_multi
combined_human-mouse_reference
14 hours ago by
tlallihuacan
• 0
0
votes
0
replies
62
views
Extracting logR and Baf files genome studio
Genomestudio
14 hours ago by
1769mkc
★ 1.3k
0
votes
1
reply
223
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
updated 16 hours ago by
chen
★ 2.5k • written 4 days ago by
Chijioke
• 0
0
votes
2
replies
405
views
Assembly issues
adapters
Assembly
Spades
updated 16 hours ago by
chen
★ 2.5k • written 28 days ago by
anna
• 0
0
votes
5
replies
439
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 16 hours ago by
chen
★ 2.5k • written 6 days ago by
k.lagan
• 0
0
votes
5
replies
1.8k
views
Fastp
fastp
updated 19 hours ago by
chen
★ 2.5k • written 3.2 years ago by
nishimalhotra2612
▴ 50
4
votes
9
replies
503
views
Need help using ExpansionHunter
ExpansionHunter
updated 7 hours ago by
GenoMax
152k • written 4 days ago by
brianhill_nc
• 0
0
votes
0
replies
87
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
21 hours ago by
decorus
• 0
0
votes
0
replies
108
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
1 day ago by
Cassandra
• 0
0
votes
1
reply
155
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT
samtools
Whole-Genome
updated 1 day ago by
GenoMax
152k • written 1 day ago by
Noah
▴ 10
0
votes
0
replies
136
views
Comparing and plotting multinomial elastic net performance
ROC
elasticnet
plotting
glmnet
machinelearning
1 day ago by
bioinfo
• 0
2
votes
3
replies
245
views
How to add gene lable on GSEA plot
gseaplot
R
updated 8 hours ago by
yura.grabovska
▴ 780 • written 1 day ago by
Emy Alade
▴ 20
0
votes
0
replies
139
views
Adding New Samples to Existing VCF Files graphtyper2
graphtyper2
existing_vcf
add_new_samples
1 day ago by
upadhyay.maulik
• 0
2
votes
5
replies
311
views
Seurat dims and QC questions
dims
updated 1 day ago by
1769mkc
★ 1.3k • written 2 days ago by
reddyornah
• 0
1
vote
1
reply
192
views
Duplication rate as reported by fastp.
fastp
duplication
RNA-seq
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Anjan
▴ 840
0
votes
2
replies
383
views
Is it appropriate to include singleton reads with paired-end datasets for low-coverage Anaplasma marginale comparative genome analysis?
assembly
analysis
coverage
genome
singletons
comparative
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
ashiqullah024
• 0
0
votes
5
replies
287
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
updated 9 hours ago by
m.sharghi
• 0 • written 2 days ago by
abedkurdi10
▴ 190
0
votes
0
replies
147
views
ComBat for Multiple Batch Effects in Methylation Data (Chip, Row, Plate)
ComBat
methylation
EPIC
batch-correction
2 days ago by
Eliveri
▴ 350
0
votes
1
reply
171
views
Using a Seurat object to create a cellchat object
cellchat
9 hours ago by
m.sharghi
• 0
0
votes
0
replies
151
views
WGCNA - High R2 and Mean connectivity at low soft power
WGCNA
2 days ago by
Leonard Barnabas
• 0
0
votes
0
replies
123
views
How do I combine or integrate my VDJ data for TCR and BCR with seurat object?
VDJ
scRepertoire
Seurat
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Jaber
▴ 30
0
votes
1
reply
282
views
DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
updated 2 days ago by
yura.grabovska
▴ 780 • written 5 days ago by
Picasa
▴ 680
2
votes
3
replies
378
views
RNA-seq: TPM batch effect correction
TPM
Combat
RNA-seq
updated 4 days ago by
rfran010
★ 1.6k • written 5 days ago by
Samuel
▴ 10
1
vote
3
replies
316
views
Error running pbrun fq2bam: No space left on device
disk
space
updated 2 days ago by
DBScan
▴ 490 • written 4 days ago by
Ritu
• 0
2
votes
3
replies
1.7k
views
How to find the annotation file for GPL16956 platform of Arraystar human lncRNA microarray V3 (Probe Name Version)?
annotation
lncRNA
microarray
probe
updated 2 days ago by
GenoMax
152k • written 5.1 years ago by
daphneolivia39
▴ 20
1
vote
5
replies
348
views
Statistics for bins
data
shotgun
updated 3 days ago by
GenoMax
152k • written 3 days ago by
shevch2009
▴ 20
5
votes
4
replies
396
views
twist exome panel analysis
twist
exome
updated 3 days ago by
GenoMax
152k • written 5 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
195
views
Run hifiasm without error correction module?
hifiasm
assembly
wgs
nanopore
genomics
updated 3 days ago by
shelkmike
★ 1.6k • written 3 days ago by
Mark
▴ 60
1
vote
1
reply
221
views
PhageTerm Galaxy
error
phageterm
genomics
updated 4 days ago by
GenoMax
152k • written 4 days ago by
NIkita
• 0
1
vote
1
reply
221
views
Demultiplexing of snAtcSeq data using demuxlet gives an empty output
genotype
demuxlet
scatacseq
demultiplexing
updated 4 days ago by
GenoMax
152k • written 4 days ago by
Bioiris
▴ 10
0
votes
1
reply
485
views
PbJelly Resume
Gap-filling
PacBio
PbJelly
written 12 months ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
170
views
How do I figure out which chain a ligand is bound to using rcsb-api?
rcsb
updated 4 days ago by
GenoMax
152k • written 4 days ago by
Priyal
▴ 10
1
vote
2
replies
345
views
Deseq2
PyDeseq2
Deseq2
updated 5 days ago by
GenoMax
152k • written 5 days ago by
sk_24
▴ 10
0
votes
0
replies
212
views
News:
In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
ChIPSeq
BisulfiteSeq
ATACSeq
workshop
5 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
234
views
News:
Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
5 days ago by
Wei
• 0
2
votes
1
reply
476
views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
CicRNA-GEO
updated 5 days ago by
rfran010
★ 1.6k • written 6 days ago by
ParastooA
▴ 20
1
vote
6
replies
450
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
5 days ago by
alejandro.mejiam1
▴ 20
0
votes
0
replies
232
views
low variant sites similarity between linear reference and vg call path
call
vg
updated 6 days ago by
GenoMax
152k • written 6 days ago by
PolenP
• 0
0
votes
0
replies
241
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization
DEG
KEGG
R
pathway
6 days ago by
txema.heredia
▴ 250
0
votes
5
replies
457
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
2 days ago by
María José
▴ 10
121,501 results • Page
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Recent Replies
Comment: MultiQC report - unique reads from sequence counts
by
rfran010
★ 1.6k
The main concern with adapter contamination is that it will eat up your sequencing costs. It should not really affect your library quality,…
Answer: Interpreting inconsistency between BLAST hits and phylogenetic clustering i
by
Mensur Dlakic
★ 29k
It depends on at least two factors: - How the alignment is done and whether the trimming is applied before tree reconstruction? If the …
Comment: Need help using ExpansionHunter
by
GenoMax
152k
Try to convert the CRAM to BAM using samtools. It should download the correct reference, if it can find it, from EBI. Otherwise you will ne…
Answer: Deg Difference in Deseq2
by
swbarnes2
15k
If the code ran at all, you probably did it correctly. Since you have such a simple design, you probably set up the design correctly. I…
Comment: How to add gene lable on GSEA plot
by
yura.grabovska
▴ 780
You're more or less there... Take a look at the ggrepel example below: https://ggrepel.slowkow.com/articles/examples#limit-labels-to-a…
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about 3/4 hours for a human wgs 30x
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Adding a comment to my question: If I have PEC and podocyte cells, and I want to study their interactions, how CellChat can be used for th…
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152k
Any time you are using a technique that enriches for a certain regions of the genome you are going to end up with duplicate reads since the…
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by
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The other thing I think about is maybe the ligands can bind to other receptors too (off-target receptors) or maybe false positives. Have yo…
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by
thomas.heigl.ibk
• 0
is it really fast? currently, i am running delly (and three other sv callers) via sv-callers and it took already 1 week and is still ongoi…
Comment: Deg Difference in Deseq2
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88k
> Or, If the deg number is wrong what can be the reasons behind that? - Truely no differences - noise and variation - underpowerment - wro…
Answer: NCBI Reference Genomes
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152k
`RefSeq` prokaryotic genomes are selected based on the criteria mentioned on this page: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryot…
Comment: NCBI Reference Genomes
by
anna
▴ 70
Thank you very much for the clarification!
Answer: NCBI Reference Genomes
by
dthorbur
★ 3.0k
It appears there is no strict threshold, but it depends on how many other assemblies for a given taxa are already submitted. I think their …
Answer: Statistical analysis in a metagenomics study to validate biological differences
by
chen
★ 2.5k
Try EasyMetagenome: https://github.com/YongxinLiu/EasyMetagenome
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