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13,516 results • Page
2 of 271
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
266
views
Highest variable features in single cell data
single-cell
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
0
votes
1
reply
210
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 3 days ago by
Scooter
▴ 280 • written 3 days ago by
Akash D
▴ 40
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 3 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
1
vote
2
replies
271
views
PCA plot
DESeq2
PCAplot
updated 1 day ago by
ATpoint
82k • written 3 days ago by
Aaliya
▴ 10
4
votes
4
replies
375
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 14 hours ago by
BioinfGuru
★ 1.7k • written 3 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 3 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
142
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
3 days ago by
4fzcgueyp5
• 0
2
votes
3
replies
311
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
240
views
Annovar using R package
Annovar
gnomAD
R
2 days ago by
DKA
▴ 40
0
votes
2
replies
220
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
biochugs
• 0
8
votes
8
replies
567
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
Aaliya
▴ 10
1
vote
8
replies
795
views
Adding CB tag to bam file
samtools
bam
updated 2 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Maria
• 0
1
vote
10
replies
933
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
3 days ago by
DKA
▴ 40
0
votes
2
replies
807
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 3 days ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
311
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 2 days ago by
GenoMax
141k • written 3 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 3 days ago by
Ram
43k • written 3 days ago by
glaciya2018
• 0
0
votes
0
replies
117
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 2 days ago by
Ram
43k • written 3 days ago by
David Langenberger
11k
0
votes
0
replies
281
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
3 days ago by
pramach1
▴ 40
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 3 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
147
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 3 days ago by
Sofia
• 0 • written 3 days ago by
mawigoj318
• 0
0
votes
0
replies
136
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
3 days ago by
salias
• 0
4
votes
7
replies
446
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 2 days ago by
dsull
★ 5.9k • written 3 days ago by
VITALA
• 0
0
votes
5
replies
306
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 13 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
116
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 3 days ago by
Ram
43k • written 3 days ago by
newuser2024
• 0
1
vote
2
replies
217
views
alignment result
RNA-seq
samtools
hisat2
2 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
112
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
101
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 3 days ago by
Ram
43k • written 3 days ago by
Jeyong
• 0
0
votes
2
replies
226
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
3 days ago by
mropri
▴ 150
2
votes
2
replies
215
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 3 days ago by
analyst
▴ 30 • written 4 days ago by
lorena9132
• 0
0
votes
0
replies
107
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
4 days ago by
Kash
▴ 110
7
votes
2
replies
269
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 4 days ago by
geneontologyhelp
▴ 390 • written 5 days ago by
catherine.teyssier
• 0
1
vote
1
reply
210
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 4 days ago by
Istvan Albert
100k • written 5 days ago by
Abeer
• 0
2
votes
4
replies
306
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
dxj294
• 0
0
votes
1
reply
150
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
246
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 3 days ago by
Ram
43k • written 4 days ago by
v.berriosfarias
▴ 140
3
votes
1
reply
222
views
Seurat merge and batch correction
Seurat
updated 4 days ago by
Ram
43k • written 5 days ago by
sooni
▴ 20
1
vote
1
reply
194
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Biostar
2.7k
1
vote
1
reply
151
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 4 days ago by
GenoMax
141k • written 4 days ago by
heelpPlease
• 0
2
votes
9
replies
842
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
509
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
2 days ago by
atowns21
• 0
0
votes
1
reply
159
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 4 days ago by
bk11
★ 2.4k • written 4 days ago by
alphaflylizard
• 0
5
votes
3
replies
250
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Estevão
• 0
0
votes
3
replies
251
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 4 days ago by
Istvan Albert
100k • written 4 days ago by
Dylan
• 0
2
votes
5
replies
296
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
1 day ago by
Lada
▴ 30
4
votes
11
replies
608
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 4 days ago by
LauferVA
4.2k • written 5 days ago by
dominickd
• 0
8
votes
16
replies
851
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 day ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
98
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
4 days ago by
ohtang7
▴ 40
3
votes
0
replies
122
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 4 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
430
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 4 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
164
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Srinka
▴ 20
13,516 results • Page
2 of 271
Recent Votes
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Recent Replies
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
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Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
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22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
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[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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