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173 results • Page
3 of 4
Sort: replies
Rank
Views
Votes
Replies
0
votes
2
replies
187
views
CreateSeuratObject taking very long
seurat
3 days ago by
eae6d2e7
• 0
0
votes
1
reply
163
views
How to decrease the motif score?
scores
Motif
updated 12 hours ago by
ATpoint
82k • written 2 days ago by
Hadia
• 0
0
votes
1
reply
125
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
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
0
votes
1
reply
141
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 6 days ago by
DBScan
▴ 310 • written 6 days ago by
brunomiwa
• 0
0
votes
1
reply
185
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 5 days ago by
andersdetermig
▴ 20 • written 6 days ago by
Christopher
• 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
3
votes
1
reply
169
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 5 days ago by
Jouni Sirén
▴ 380 • written 5 days ago by
StevieP
▴ 10
0
votes
1
reply
156
views
How to get 2 seurat objects into a DEseq
Seurat
DEseq
updated 5 days ago by
Ram
44k • written 5 days ago by
He11oJe11o
• 0
0
votes
1
reply
133
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 5 days ago by
Ram
44k • written 5 days ago by
ashkan
▴ 160
0
votes
1
reply
148
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Fossil
• 0
0
votes
1
reply
270
views
GWAS Phenotypes
GWAS
updated 4 days ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
1
vote
1
reply
137
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
151
views
Free AI for R programming
R
updated 4 days ago by
Ram
44k • written 4 days ago by
mohamadzare6022
▴ 10
0
votes
1
reply
134
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 4 days ago by
Ram
44k • written 5 days ago by
avelarbio46
▴ 30
0
votes
1
reply
160
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 4 days ago by
Papyrus
★ 2.9k • written 4 days ago by
June
• 0
0
votes
1
reply
167
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 4 days ago by
Ram
44k • written 4 days ago by
a.bibek52
▴ 10
0
votes
1
reply
196
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 4 days ago by
jared.andrews07
★ 17k • written 4 days ago by
atan
• 0
4
votes
1
reply
235
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
May Ling
• 0
0
votes
1
reply
184
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 3 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
Maksim
• 0
0
votes
1
reply
205
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 3 days ago by
Bastien Hervé
5.3k • written 3 days ago by
bio_info
▴ 20
2
votes
1
reply
200
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 3 days ago by
Jeremy Leipzig
22k • written 3 days ago by
liaotsungjen
▴ 10
0
votes
1
reply
391
views
LDhat lookup table
LDhat
updated 3 days ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
1
reply
3.0k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 3 days ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
256
views
Annotating single cell data automatically
single-cell
updated 3 days ago by
Ram
44k • written 5 weeks ago by
Gerard
• 0
0
votes
1
reply
175
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 3 days ago by
Ram
44k • written 3 days ago by
garcesj
▴ 50
0
votes
1
reply
150
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
updated 20 hours ago by
jared.andrews07
★ 17k • written 1 day ago by
sc_analysis
• 0
0
votes
1
reply
189
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 8 hours ago by
raphael.B
▴ 520 • written 3 days ago by
irebekah.c
• 0
0
votes
1
reply
82
views
Salmon vs Kallisto vs RSEM
quantification
kallisto
Salmon
transcriptomic
RSEM
updated 4 hours ago by
Rob
6.6k • written 6 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
135
views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
polygenic-risk-score
imputation
updated 3 days ago by
Ram
44k • written 3 days ago by
kl
▴ 10
0
votes
0
replies
115
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
2 days ago by
adi.gershon1
• 0
0
votes
0
replies
132
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 3 days ago by
Ram
44k • written 3 days ago by
Alessia
• 0
0
votes
0
replies
117
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 2 days ago by
Pierre Lindenbaum
162k • written 2 days ago by
elbakri.fatimazahrae
• 0
0
votes
0
replies
161
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
3 days ago by
doramora
▴ 10
0
votes
0
replies
93
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
130
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
3 days ago by
Emily
▴ 20
0
votes
0
replies
199
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
3 days ago by
mtabaka
• 0
0
votes
0
replies
158
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 3 days ago by
Ram
44k • written 4 days ago by
Christopher
▴ 10
0
votes
0
replies
134
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 4 days ago by
GenoMax
142k • written 4 days ago by
jway
• 0
0
votes
0
replies
81
views
Tubemap multiseq
vg
1 day ago by
karciharun42
• 0
2
votes
0
replies
218
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
4 days ago by
Matthias Zepper
4.6k
0
votes
0
replies
94
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 4 days ago by
Ram
44k • written 4 days ago by
emmanouil.a
▴ 120
0
votes
0
replies
91
views
GWAS or QTL mapping in RIL population
GWAS
RIL
4 days ago by
韩雨
• 0
0
votes
0
replies
64
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
4 days ago by
Linus
• 0
0
votes
0
replies
63
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
21 hours ago by
kl
▴ 10
0
votes
0
replies
94
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
6 days ago by
Ayda Ecem
• 0
0
votes
0
replies
70
views
Determining rs ids from SNP HGV base ID?
base
RsID
SNP
ID
HGV
19 hours ago by
Katherine
• 0
0
votes
0
replies
120
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
4 days ago by
Tim
• 0
0
votes
0
replies
102
views
Extracting haplotype-specific annotations from splicing graph
vg
4 days ago by
Juhyun
• 0
0
votes
0
replies
54
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
12 hours ago by
s
• 0
173 results • Page
3 of 4
Recent Votes
Comment: Functional enrichment analysis for unique gene IDs
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
How do i calculate the mean of triplicates in a data.frame based on pattern?
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
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Comment: Venter Genome Vcf
by
Jeremy Leipzig
22k
there are some violations in this VCF: - Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=St…
Answer: Cut&Run and heatmap
by
sogand
• 0
Hi all, I am new to cut&run or any peak-related analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt …
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Since the locus-tags are unclassified, I used the CDS instead of the locus-tags to retrive their ensembl IDs using ensembl bacteria website…
Comment: samtools mpileup error - 1 samples in 1 input files
by
Damla
• 0
Could you find a solution to your problem?
Comment: txt file to bigwig
by
sogand
• 0
Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
Answer: Help me with Heatmap
by
MolGeek
▴ 50
Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
Answer: Help me with simple data for RNA seq
by
swbarnes2
14k
1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
Comment: identify the coordinate for coding and non_coding region.
by
Ghada
• 0
mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
Comment: identify the coordinate for coding and non_coding region.
by
GenoMax
142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
Answer: Salmon vs Kallisto vs RSEM
by
Rob
6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Mike Smith
★ 2.0k
In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
Answer: Download All The Bacterial Genomes From Ncbi
by
2284046470
• 0
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
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://rdatatable.gitlab.io/data.table/): ``` library(data.table) dat <- structure(list(sgrna = c("Cont…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
Assa Yeroslaviz
★ 1.9k
I know it can be done with something like that: ``` cbind(p767.AM = (rowMeans(p767[,2:4])), p767.MM = (rowMeans(p767[,5:7]…
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