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116,584 results • Page
1 of 2332
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Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
1 minute ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
1
view
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
just now by
David Langenberger
11k
0
votes
0
replies
8
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
15 minutes ago by
pramach1
▴ 40
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 1 hour ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
0
replies
26
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
2 hours ago by
mawigoj318
• 0
0
votes
0
replies
53
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
4 hours ago by
salias
• 0
3
votes
4
replies
159
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 2 hours ago by
ATpoint
82k • written 8 hours ago by
VITALA
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
2
replies
81
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated 1 hour ago by
Istvan Albert
100k • written 4 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
40
views
Alternative splicing
single-cell
suppa
rnaseq
splicing
alternative
5 hours ago by
newuser2024
• 0
0
votes
0
replies
35
views
Network Alignment
plugin
Cytoscape
CytoMCS
5 hours ago by
Akash D
▴ 40
0
votes
1
reply
66
views
alignment result
RNA-seq
samtool
analysis
hisat2
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
40
views
News:
hands-on introduction to generalized linear models (GLMs) using R
GeneralizedLinearModels
GLMs
R
7 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
42
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
hetero
Seurat
modelHomotypic
DoubletFinder
7 hours ago by
Jeyong
• 0
0
votes
0
replies
64
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
9 hours ago by
Aaliya
• 0
0
votes
2
replies
126
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
1 hour ago by
mropri
▴ 150
2
votes
2
replies
129
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 9 hours ago by
analyst
▴ 30 • written 14 hours ago by
lorena9132
• 0
0
votes
0
replies
58
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
14 hours ago by
Kash
▴ 110
7
votes
2
replies
197
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 15 hours ago by
geneontologyhelp
▴ 390 • written 1 day ago by
catherine.teyssier
• 0
0
votes
1
reply
145
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 15 hours ago by
Istvan Albert
100k • written 1 day ago by
Abeer
• 0
0
votes
4
replies
222
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
dxj294
• 0
0
votes
1
reply
95
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 16 hours ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
172
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 5 hours ago by
b.contreras.moreira
▴ 170 • written 16 hours ago by
v.berriosfarias
▴ 140
2
votes
1
reply
149
views
Seurat merge and batch correction
Seurat
updated 17 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
1
vote
1
reply
116
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 17 hours ago by
Pierre Lindenbaum
161k • written 17 hours ago by
Biostar
2.7k
1
vote
1
reply
100
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 18 hours ago by
GenoMax
141k • written 18 hours ago by
heelpPlease
• 0
2
votes
9
replies
767
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 13 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
333
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
10 hours ago by
atowns21
• 0
0
votes
1
reply
109
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 18 hours ago by
bk11
★ 2.3k • written 19 hours ago by
alphaflylizard
• 0
3
votes
3
replies
167
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 19 hours ago by
GenoMax
141k • written 20 hours ago by
Estevão
• 0
0
votes
3
replies
188
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 15 hours ago by
Istvan Albert
100k • written 21 hours ago by
Dylan
• 0
1
vote
2
replies
96
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
18 minutes ago by
Lada
▴ 30
4
votes
11
replies
444
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 13 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
3
votes
8
replies
450
views
How to convert plink files to Hapmap Format
GWAS
Plink
55 minutes ago by
Sofia
• 0
0
votes
0
replies
66
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
22 hours ago by
ohtang7
▴ 40
3
votes
0
replies
86
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 22 hours ago by
Ram
43k • written 23 hours ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
383
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
122
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
8
votes
5
replies
4.8k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
5
replies
237
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 hours ago by
njornet
▴ 20
5
votes
4
replies
590
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
8 hours ago by
kirillkirilenko
▴ 40
0
votes
0
replies
70
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 22 hours ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
3
replies
343
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 1 day ago by
colindaven
6.4k • written 9 days ago by
rj.rezwan
• 0
0
votes
0
replies
80
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
1
vote
3
replies
180
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
0
votes
3
replies
180
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 1 day ago by
mchour
• 0 • written 1 day ago by
rhossen
• 0
1
vote
1
reply
140
views
WGCNA preservation analysis
WGCNA
preservation
updated 1 day ago by
Michael
54k • written 1 day ago by
michael.flower.14
▴ 180
1
vote
3
replies
217
views
some error in building kraken2 database
metagenome
kraken2
12 hours ago by
Art1ess
• 0
0
votes
1
reply
114
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 22 hours ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
118
views
Plots for DNA methylation data
plots
DNA
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sarahawan92
▴ 10
116,584 results • Page
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Recent Votes
Comment: How to trim transcripts using information from NCBI contamination screen report
Difference Between "Mate Pair" And "Pair-End"
Difference Between "Mate Pair" And "Pair-End"
Comment: To get p-values for the TPM
Comment: HaplotypeCaller - only SNPs
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
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Recent Replies
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data
by
GenoMax
141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
by
GenoMax
141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
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