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116,589 results • Page
1 of 2332
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Votes
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0
votes
0
replies
14
views
Can you give me an example of a protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 hour ago by
4fzcgueyp5
• 0
1
vote
3
replies
158
views
clustalo - align milions of short seq, memory issue
memory
clustalo
1 hour ago by
emmanouil.a
▴ 120
0
votes
1
reply
56
views
Annovar using R package
Annovar
gnomAD
R
updated 1 hour ago by
Pierre Lindenbaum
161k • written 4 hours ago by
DKA
▴ 40
0
votes
2
replies
101
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 2 hours ago by
Mensur Dlakic
★ 27k • written 5 hours ago by
biochugs
• 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
3
votes
6
replies
281
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 4 hours ago by
swbarnes2
14k • written 19 hours ago by
Aaliya
▴ 10
0
votes
6
replies
595
views
Adding CB tag to bam file
samtools
bam
updated 4 hours ago by
swbarnes2
14k • written 6 days ago by
Maria
• 0
1
vote
10
replies
817
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
5 hours ago by
DKA
▴ 40
0
votes
0
replies
47
views
Finding orthologs between genome error
OMA
OMAbrowser
6 hours ago by
hemantcnaik
• 0
0
votes
2
replies
730
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 7 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
3
replies
142
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 8 hours ago by
GenoMax
141k • written 10 hours ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
64
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 5 hours ago by
Ram
43k • written 10 hours ago by
glaciya2018
• 0
0
votes
0
replies
50
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
10 hours ago by
David Langenberger
11k
0
votes
0
replies
81
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
10 hours ago by
pramach1
▴ 40
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 11 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
91
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 8 hours ago by
Sofia
• 0 • written 12 hours ago by
mawigoj318
• 0
0
votes
0
replies
73
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
14 hours ago by
salias
• 0
4
votes
5
replies
261
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 7 hours ago by
swbarnes2
14k • written 18 hours ago by
VITALA
• 0
0
votes
2
replies
135
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 hours ago by
Ram
43k • written 15 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
64
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 5 hours ago by
Ram
43k • written 15 hours ago by
newuser2024
• 0
0
votes
0
replies
56
views
Network Alignment
plugin
Cytoscape
CytoMCS
15 hours ago by
Akash D
▴ 40
0
votes
1
reply
104
views
alignment result
RNA-seq
samtools
hisat2
updated 5 hours ago by
Ram
43k • written 16 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
61
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 5 hours ago by
Ram
43k • written 17 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
56
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 5 hours ago by
Ram
43k • written 18 hours ago by
Jeyong
• 0
0
votes
2
replies
167
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
11 hours ago by
mropri
▴ 150
2
votes
2
replies
149
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 19 hours ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
71
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
7
votes
2
replies
217
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
1
reply
161
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Abeer
• 0
0
votes
4
replies
240
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
dxj294
• 0
0
votes
1
reply
109
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 20 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
192
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 5 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
1
reply
167
views
Seurat merge and batch correction
Seurat
updated 1 day ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
1
vote
1
reply
138
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Biostar
2.7k
1
vote
1
reply
113
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 1 day ago by
GenoMax
141k • written 1 day ago by
heelpPlease
• 0
2
votes
9
replies
784
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 23 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
348
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
21 hours ago by
atowns21
• 0
0
votes
1
reply
123
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
3
votes
3
replies
183
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
0
votes
3
replies
202
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
Dylan
• 0
1
vote
4
replies
205
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 7 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
4
votes
11
replies
460
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 23 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
3
votes
13
replies
620
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 8 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
79
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
3
votes
0
replies
99
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
398
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
135
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
4.9k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
5
replies
259
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
13 hours ago by
njornet
▴ 20
5
votes
4
replies
610
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
18 hours ago by
kirillkirilenko
▴ 40
116,589 results • Page
1 of 2332
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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★ 2.5k
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Answer: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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