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181 results • Page
2 of 4
Sort: Votes
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Views
Votes
Replies
1
vote
4
replies
320
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 6 days ago by
Ram
44k • written 6 days ago by
Harshita
• 0
1
vote
2
replies
241
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
Varsha
• 0
1
vote
1
reply
134
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 3 days ago by
GenoMax
142k • written 3 days ago by
azeu
▴ 10
1
vote
4
replies
406
views
some error in building kraken2 database
metagenome
kraken2
updated 3 days ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
1
vote
3
replies
311
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
5 days ago by
Pegasus
▴ 100
1
vote
3
replies
569
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 5 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
1
vote
6
replies
376
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
5 days ago by
Umer
▴ 50
1
vote
2
replies
201
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 6 days ago by
Ram
44k • written 7 days ago by
Sony
▴ 10
1
vote
10
replies
641
views
Add stats to the plot
R
5 days ago by
Ghada
• 0
1
vote
3
replies
260
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 6 days ago by
GenoMax
142k • written 8 days ago by
KHURRAM SHAHZAD
• 0
1
vote
3
replies
320
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 3 days ago by
Jeremy
▴ 910 • written 4 days ago by
Mohamed Samir
▴ 30
1
vote
3
replies
205
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 4 days ago by
GenoMax
142k • written 5 days ago by
s
• 0
1
vote
2
replies
241
views
Construction of circos plot from WGS data
WGS
Circos
3 days ago by
Anitha
▴ 10
1
vote
3
replies
236
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Wilber0x
▴ 50
1
vote
2
replies
193
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 5 days ago by
Ram
44k • written 5 days ago by
Harshita
• 0
1
vote
2
replies
267
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 days ago by
F110152169
• 0
1
vote
2
replies
396
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 5 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
2
replies
218
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
6 days ago by
ojaswinipandey
• 0
1
vote
4
replies
322
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 5 days ago by
Ram
44k • written 12 days ago by
Arton
▴ 10
1
vote
1
reply
137
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 6 days ago by
GenoMax
142k • written 6 days ago by
niruf
• 0
1
vote
4
replies
301
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
2 days ago by
sc_analysis
• 0
1
vote
2
replies
244
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
Dr.
• 0
1
vote
2
replies
313
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
1 day ago by
peanut
• 0
1
vote
3
replies
265
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
Sara
▴ 30
1
vote
3
replies
910
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 4 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
1
vote
10
replies
3.6k
views
Merging multiple samples in Seurat
scRNA-seq
snRNA-seq
RNA-seq
Seurat
updated 1 day ago by
Picasa
▴ 640 • written 7 months ago by
AFP3
• 0
1
vote
3
replies
208
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 5 days ago by
Pierre Lindenbaum
162k • written 5 days ago by
mrk
• 0
1
vote
2
replies
195
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 15 hours ago by
LauferVA
4.2k • written 2 days ago by
carolofharvest
▴ 40
1
vote
4
replies
285
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
5 days ago by
shpak.max
▴ 50
1
vote
1
reply
741
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
1
vote
7
replies
383
views
samtools write-index
samtools
5 hours ago by
R.L.
• 0
1
vote
2
replies
228
views
Failed to download data from EBI with ascp
EBI
aspera
updated 2 hours ago by
孝中
• 0 • written 6 weeks ago by
biock
▴ 60
1
vote
0
replies
16
views
Search within posts based on tags using the Biostars API
api
biostars
54 minutes ago by
Bálint
▴ 10
0
votes
5
replies
237
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
2 days ago by
Deepthi
• 0
0
votes
3
replies
334
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
2 days ago by
Brian Bushnell
20k
0
votes
0
replies
108
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 days ago by
F110152169
• 0
0
votes
0
replies
304
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
2 days ago by
Sony
▴ 10
0
votes
0
replies
97
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
1 day ago by
adi.gershon1
• 0
0
votes
0
replies
99
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 1 day ago by
Pierre Lindenbaum
162k • written 1 day ago by
elbakri.fatimazahrae
• 0
0
votes
0
replies
73
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
PopulationGenomics
GenotypeLikelihoods
Low-Coverage
ANGSD
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
60
views
Tubemap multiseq
vg
15 hours ago by
karciharun42
• 0
0
votes
0
replies
42
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
9 hours ago by
kl
▴ 10
0
votes
1
reply
112
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
updated 9 hours ago by
jared.andrews07
★ 17k • written 18 hours ago by
sc_analysis
• 0
0
votes
0
replies
43
views
Determining rs ids from SNP HGV base ID?
base
RsID
SNP
ID
HGV
7 hours ago by
Katherine
• 0
0
votes
0
replies
12
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
1 hour ago by
s
• 0
0
votes
1
reply
141
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
updated 1 hour ago by
b.contreras.moreira
▴ 200 • written 2 days ago by
marco.barr
▴ 130
0
votes
1
reply
112
views
How to decrease the motif score?
scores
Motif
updated 41 minutes ago by
ATpoint
82k • written 1 day ago by
Hadia
• 0
0
votes
4
replies
269
views
GO analysis: p-value range
GO
R
updated 6 days ago by
Matthias Zepper
4.6k • written 7 days ago by
sooni
▴ 20
0
votes
2
replies
158
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
30 minutes ago by
Sara
▴ 30
0
votes
1
reply
148
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 6 days ago by
marco.barr
▴ 130 • written 6 days ago by
sooni
▴ 20
181 results • Page
2 of 4
Recent Votes
Extract ENSEMBL IDs from processed Seurat object instead of gene symbols
Answer: Extract ENSEMBL IDs from processed Seurat object instead of gene symbols
Comment: Invalid CIGAR after using bam clipOverlap
Comment: Invalid CIGAR after using bam clipOverlap
Invalid CIGAR after using bam clipOverlap
NCBI BLAST+ 2.14.1 Now Available
Answer: extract only geneID and gene symbol from GTF file
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Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score?
by
ATpoint
82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig
by
b.contreras.moreira
▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
please, show us the following output: samtools view "${Ind1}_sorted_dup.bam" | grep -F "A00152:841:H7J22DRX3:2:1112:5267:11397" Furth…
Comment: Failed to download data from EBI with ascp
by
孝中
• 0
Hi, have you found the solution to this problem?
Comment: samtools write-index
by
R.L.
• 0
Oh God, thank you so much for helping me in both platforms! I am gonna upgrade my samtools to stay tracked with you and your team! Thank yo…
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR
by
jared.andrews07
★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
Couldn't tell you, I avoid Seurat like the plague.
Comment: What is the best practice of scRNA workflow for multiple patients and samples us
by
Picasa
▴ 640
Same. did you get any solution ?
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
LauferVA
4.2k
Generally, I cannot advise this in the abstract. The thing is, depending on the treatment group and so forth, there are some transcripts th…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
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