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84 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 6 days ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
1
vote
6
replies
376
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
6 days ago by
Umer
▴ 50
0
votes
5
replies
249
views
Why most genes have high padj values
RNA-seq
DEG
updated 6 days ago by
Ram
44k • written 7 days ago by
mnx0723
• 0
3
votes
4
replies
162
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
6 hours ago by
MboiTui
▴ 20
1
vote
4
replies
408
views
some error in building kraken2 database
metagenome
kraken2
updated 4 days ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
1
vote
4
replies
307
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
0
votes
4
replies
250
views
Where to find old version of GATK best practice
gatk
5 days ago by
Zhenyu Zhang
★ 1.2k
0
votes
4
replies
378
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
3 days ago by
mavy
▴ 10
0
votes
4
replies
244
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
5 days ago by
shpak.max
▴ 50
0
votes
4
replies
342
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
5 days ago by
Luqman
• 0
0
votes
3
replies
180
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 5 days ago by
Ram
44k • written 6 days ago by
pirku
• 0
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 6 days ago by
marco.barr
▴ 130 • written 7 days ago by
Mohamed Samir
▴ 30
0
votes
3
replies
359
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 3 days ago by
ATpoint
82k • written 3 days ago by
shahzaibali
• 0
1
vote
3
replies
206
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 5 days ago by
GenoMax
142k • written 5 days ago by
s
• 0
0
votes
2
replies
247
views
What do the transcript variant # mean in RefSeq?
refseq
updated 3 days ago by
Ram
44k • written 3 days ago by
curious
▴ 750
0
votes
2
replies
214
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
5 days ago by
Shukai
• 0
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
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
0
votes
2
replies
195
views
vcf phasing
beagle
WhatsHap
phasing
5 days ago by
safeassli
▴ 10
1
vote
2
replies
251
views
Failed to download data from EBI with ascp
EBI
aspera
updated 7 hours ago by
孝中
• 0 • written 6 weeks ago by
biock
▴ 60
1
vote
2
replies
205
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 21 hours ago by
LauferVA
4.2k • written 2 days ago by
carolofharvest
▴ 40
0
votes
2
replies
189
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
2 hours ago by
marco.barr
▴ 130
1
vote
2
replies
275
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
3 days ago by
F110152169
• 0
0
votes
2
replies
432
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
5 days ago by
ezz3
• 0
0
votes
2
replies
290
views
How can I calculate the OS of each patient?
overall-survival
6 days ago by
Pedro
• 0
0
votes
2
replies
186
views
CreateSeuratObject taking very long
seurat
3 days ago by
eae6d2e7
• 0
0
votes
2
replies
680
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 3 days ago by
June
• 0 • written 10 months ago by
rkb965
• 0
1
vote
1
reply
135
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 4 days ago by
GenoMax
142k • written 4 days ago by
azeu
▴ 10
0
votes
1
reply
124
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 6 days ago by
Pierre Lindenbaum
162k • written 6 days ago by
Peter Chung
▴ 200
0
votes
1
reply
140
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 5 days ago by
DBScan
▴ 310 • written 6 days ago by
brunomiwa
• 0
0
votes
1
reply
156
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 5 days ago by
ATpoint
82k • written 5 days ago by
rj.rezwan
• 0
0
votes
1
reply
133
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 4 days ago by
Ram
44k • written 5 days ago by
ashkan
▴ 160
0
votes
1
reply
145
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Fossil
• 0
0
votes
1
reply
150
views
Free AI for R programming
R
updated 3 days ago by
Ram
44k • written 4 days ago by
mohamadzare6022
▴ 10
0
votes
1
reply
132
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 3 days ago by
Ram
44k • written 4 days ago by
avelarbio46
▴ 30
0
votes
1
reply
159
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 3 days ago by
Papyrus
★ 2.9k • written 3 days ago by
June
• 0
0
votes
1
reply
165
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 3 days ago by
Ram
44k • written 3 days ago by
a.bibek52
▴ 10
0
votes
1
reply
196
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 2 days ago by
Bastien Hervé
5.3k • written 3 days ago by
bio_info
▴ 20
0
votes
1
reply
382
views
LDhat lookup table
LDhat
updated 2 days ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
1
reply
163
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 2 days ago by
Ram
44k • written 2 days ago by
garcesj
▴ 50
0
votes
1
reply
145
views
How to decrease the motif score?
scores
Motif
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Hadia
• 0
0
votes
1
reply
148
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 1 hour ago by
raphael.B
▴ 520 • written 3 days ago by
irebekah.c
• 0
0
votes
0
replies
105
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 4 days ago by
Ram
44k • written 4 days ago by
Melissa
• 0
0
votes
0
replies
120
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
4 days ago by
RD
▴ 10
0
votes
0
replies
94
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 3 days ago by
Ram
44k • written 4 days ago by
emmanouil.a
▴ 120
0
votes
0
replies
35
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
6 hours ago by
s
• 0
0
votes
0
replies
90
views
Rescaling normalized enrichment score (NES)
heatmap
5 days ago by
CTLong
▴ 110
0
votes
0
replies
104
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 6 days ago by
Ram
44k • written 7 days ago by
ev97
▴ 20
0
votes
0
replies
47
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
35 minutes ago by
Ghada
• 0
1
vote
0
replies
51
views
Search within posts based on tags using the Biostars API
api
meta
biostars
4 hours ago by
Bálint
▴ 10
84 results • Page
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Recent Votes
C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
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Recent Replies
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
dariober
14k
I'm a happy user of [data.table](https://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.html): ``` library(data.tabl…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
Assa Yeroslaviz
★ 1.8k
I know it can be done with something like that: ``` cbind(p767.AM = (rowMeans(p767[,2:4])), p767.MM = (rowMeans(p767[,5:7]…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
ATpoint
82k
Why is your `GeneName` column in mapped a mix of Ensembl IDs and gene names? What Jared wants to say is that during the preprocessing you s…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
GenoMax
142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file
by
raphael.B
▴ 520
You have a space in your reference path. Not sure it's intended?
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Do you have any recommendations of such sources or how to search for them? I'm a newbie and I need to convert GRCh38 Ensembl IDs to Entrez …
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Shred
★ 1.4k
Genecards added a footer saying that >SCRAPING AND OTHER AUTOMATED DOWNLOAD AND USE OF GENECARDS DATA STRICTLY PROHIBITED While this is …
Comment: perl Error - needLargeMem Bigwig
by
marco.barr
▴ 130
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I h…
Answer: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Here's a slightly changed version of this script. I changed line 42 from `'title':'NCBI Entrez Gene'` to `'title':'NCBI Gene'` ). And…
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection
by
a.alnawfal.1992
▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
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>
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