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116,598 results • Page
1 of 2332
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Votes
Replies
0
votes
0
replies
7
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
10 minutes ago by
QX
• 0
0
votes
1
reply
25
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
23 minutes ago by
Assa Yeroslaviz
★ 1.8k
2
votes
1
reply
85
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 1 hour ago by
Adrian Altenhoff
★ 1.1k • written 17 hours ago by
hemantcnaik
• 0
0
votes
0
replies
16
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 hour ago by
Aspire
▴ 300
2
votes
4
replies
112
views
Fetch table from clinvar database according to a list of rsid
clinvar
fetching
data
python
perl
1 hour ago by
ashaneev07
▴ 20
1
vote
2
replies
58
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
2 minutes ago by
analyst
▴ 30
0
votes
1
reply
71
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 3 hours ago by
b.contreras.moreira
▴ 170 • written 4 hours ago by
Broccoli
• 0
0
votes
2
replies
68
views
Highest variable features in single cell data
cell
single
21 minutes ago by
Kazo
• 0
0
votes
1
reply
116
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 6 hours ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
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
2
votes
4
replies
2.3k
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 6 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
0
replies
55
views
PCA plot
DESeq2
PCAplot
7 hours ago by
Aaliya
▴ 10
0
votes
0
replies
52
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
7 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
241
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 8 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 8 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
63
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
9 hours ago by
4fzcgueyp5
• 0
2
votes
3
replies
228
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
120
views
Annovar using R package
Annovar
gnomAD
R
updated 11 hours ago by
Pierre Lindenbaum
161k • written 14 hours ago by
DKA
▴ 40
0
votes
2
replies
147
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 12 hours ago by
Mensur Dlakic
★ 27k • written 15 hours ago by
biochugs
• 0
3
votes
8
replies
413
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 5 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
1
vote
8
replies
686
views
Adding CB tag to bam file
samtools
bam
updated 2 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
1
vote
10
replies
860
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
15 hours ago by
DKA
▴ 40
0
votes
2
replies
751
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 18 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
4
replies
185
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
3 hours ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
89
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 15 hours ago by
Ram
43k • written 20 hours ago by
glaciya2018
• 0
0
votes
0
replies
74
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
20 hours ago by
David Langenberger
11k
0
votes
0
replies
146
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
20 hours ago by
pramach1
▴ 40
0
votes
14
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 21 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
108
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 19 hours ago by
Sofia
• 0 • written 23 hours ago by
mawigoj318
• 0
0
votes
0
replies
94
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
4
votes
7
replies
335
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 2 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
4
replies
180
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
2 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
83
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 15 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
154
views
alignment result
RNA-seq
samtools
hisat2
4 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
79
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 15 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
75
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 15 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
187
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
21 hours ago by
mropri
▴ 150
2
votes
2
replies
173
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 1 day ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
86
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
7
votes
2
replies
236
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
180
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
260
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
125
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
212
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 15 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
1
reply
185
views
Seurat merge and batch correction
Seurat
updated 1 day ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
1
vote
1
reply
156
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
129
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
802
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
372
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
141
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
116,598 results • Page
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Recent Votes
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
Answer: is oxford nanopore technology data paired or single end sequencing?
Answer: Trying to wrap my head around Illumina paired end sequencing
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Assa Yeroslaviz
★ 1.8k
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Keem Uarren Eiryll
• 0
Centurion
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Recent Replies
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
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