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116,841 results • Page
1 of 2337
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How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
10 minutes ago by
Lila M
★ 1.2k
0
votes
0
replies
12
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
40 minutes ago by
Shae
• 0
0
votes
1
reply
70
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 2 hours ago by
marco.barr
▴ 90 • written 11 hours ago by
odi
▴ 10
0
votes
4
replies
87
views
Importing a fastq file
Fastq
2 hours ago by
oumo
• 0
0
votes
6
replies
2.0k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 2 hours ago by
zylcc2
• 0 • written 3.2 years ago by
gs000095
▴ 10
795
votes
167
replies
143k
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
0
votes
1
reply
40
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 2 hours ago by
andres.firrincieli
3.6k • written 3 hours ago by
kacollier
▴ 30
0
votes
0
replies
36
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
variant
4 hours ago by
ashaneev07
▴ 20
1
vote
2
replies
1.4k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 6 hours ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
45
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 6 hours ago by
Ram
43k • written 7 hours ago by
curious_butterfly
• 0
0
votes
0
replies
51
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
17 minutes ago by
Zeng Hao
▴ 40
0
votes
1
reply
88
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
rackbersingh
• 0
0
votes
1
reply
95
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 10 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
Matthew
• 0
0
votes
1
reply
83
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 6 hours ago by
Ram
43k • written 11 hours ago by
cput
• 0
0
votes
0
replies
64
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
11 hours ago by
asalimih
▴ 60
0
votes
4
replies
292
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
13 hours ago by
schmince
• 0
0
votes
2
replies
119
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated just now by
i.sudbery
19k • written 13 hours ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 14 hours ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
1
reply
118
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 14 hours ago by
marco.barr
▴ 90 • written 16 hours ago by
elisheva
▴ 120
0
votes
0
replies
58
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 12 hours ago by
Ram
43k • written 16 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
210
views
Seurat V5 integration
Seurat
integration
updated 12 hours ago by
Ram
43k • written 3 days ago by
starswillfade
▴ 10
0
votes
2
replies
171
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 12 hours ago by
Ram
43k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
74
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 12 hours ago by
Ram
43k • written 17 hours ago by
carlopecoraro2
★ 2.5k
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 18 hours ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
0
votes
2
replies
114
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
madders73
• 0
4
votes
2
replies
202
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
7 hours ago by
mnx0723
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 21 hours ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.4k
0
votes
3
replies
207
views
RNA seq analysis
DESeq
RNA-seq
updated 14 hours ago by
Ram
43k • written 21 hours ago by
prifa
• 0
10
votes
3
replies
256
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 22 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
ijarne
• 0
0
votes
0
replies
105
views
Chance for trained without experience
bio
updated 22 hours ago by
ATpoint
82k • written 22 hours ago by
shehab
• 0
1
vote
2
replies
148
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
23 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
80
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
1 day ago by
Omics data mining
▴ 260
0
votes
2
replies
136
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
22 hours ago by
njornet
▴ 20
0
votes
2
replies
163
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 17 hours ago by
Adam
▴ 30 • written 1 day ago by
Darya
• 0
0
votes
5
replies
203
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 21 hours ago by
Joe
21k • written 1 day ago by
Lemonhope
• 0
0
votes
0
replies
118
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
2 hours ago by
Winter
• 0
0
votes
5
replies
250
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
18 hours ago by
me
• 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
1
reply
108
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
72
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
1 day ago by
analyst
▴ 50
0
votes
0
replies
71
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
1 day ago by
usa.cd.genomics
• 0
0
votes
0
replies
75
views
Blog:
Overview of Nanopore Sequencing
biotech
1 day ago by
usa.cd.genomics
• 0
0
votes
0
replies
84
views
meffil.snp.concordance
meffil
methylation
snp_concordance
1 day ago by
kyj222637
• 0
0
votes
1
reply
124
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 18 hours ago by
Bastien Hervé
5.3k • written 1 day ago by
sooni
▴ 20
1
vote
5
replies
391
views
HCL database download
HCL
updated 1 day ago by
Ram
43k • written 5 days ago by
sooni
▴ 20
0
votes
1
reply
238
views
barcode of TCR-sequencing
barcode
updated 1 day ago by
mizraelson
▴ 60 • written 8 days ago by
yueli7
▴ 250
0
votes
3
replies
199
views
STAR aligner error
RNA-seq
STAR
slurm
updated 14 hours ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
0
replies
88
views
monocle 3-- Could not get node in small cluster
monocle3
1 day ago by
synat.keam
▴ 100
0
votes
2
replies
185
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
18 hours ago by
Nicholas
• 0
1
vote
4
replies
344
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
1 day ago by
heelpPlease
• 0
116,841 results • Page
1 of 2337
Recent Votes
Comment: Problem with Seurat package in PercentageFeatureSet function
Answer: Can I merge Hi-C fastq files from different lanes?
A: How to get SNP identifiers from VCF file?
Answer: How can I analyze normalized expression data?
Answer: How can I analyze normalized expression data?
Answer: Pruning Phylogenetic Trees and Bootstrap Values
Difference between Pysam Pileup and Fetch
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Comment: Pluritest for pluripotency broken
by
DGTool
• 0
Hi, just a question, were you able to find a way to get it to work locally? My understanding from looking around seems to be at least so fa…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
Yoosef
▴ 60
Thanks a lot for your response. Today, I finally understood what my problem was. I have used CreateAssayObject function, while I should ha…
Comment: Correlation Analysis
by
Researcher
▴ 30
there is only one value of methylation and expression per gene. I did perform corr(gene_corr$methylation_values, gene_corr$expression_value…
Answer: Enhanced Volcano-Cut off
by
marco.barr
▴ 90
from the documentation it seems that it reports limits for the value of log2 fold-change in an absolute sense. FCcutoff: Cut-off for…
Answer: Importing a fastq file
by
oumo
• 0
The fastq file is in my local disk, and I want to upload it to Ubuntu
Comment: Conda severely broken after attempting mamba install
by
andres.firrincieli
3.6k
I have been there... I just reinstalled conda.
Comment: Importing a fastq file
by
marco.barr
▴ 90
That's right.. With `cp` command from terminal cp /mnt/c/path/to/your/fastq/file.fastq /path/in/wsl/
Comment: Copy number Variation analysis using conumee
by
zylcc2
• 0
if your seqnames include "chrX" or "chrY", should add "chrXY=TRUE". like this : anno_combine <- CNV.create_anno(bin_minprobes = 15, bin_min…
Comment: Importing a fastq file
by
ATpoint
82k
Windows is mounted as `/mnt/c/...` in WSL (at least in WSL2).
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marco.barr
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Can you explain better what you mean? If I understand correctly, your fastq file must be in the Ubuntu home folder of your wsl to be able t…
Answer: Seurat CellCycleScoring – confused about the proper order of operations when usi
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Li
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I‘m not an expert in sctransform or cellcyclescoring. But I think it's because sctransform creates a new assay named "SCT", which is differ…
Comment: How can I analyze normalized expression data?
by
mnx0723
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thank you for comment
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
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▴ 40
Dear Klaus, Thank you for the reply. If I could clarify with an example: With this tree, B0----------------- A -| B1----------…
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Feels a bit strange for an aptitude test, feels more like homework. 1) seems OK to me, just chuck them into CAP3 and see what falls out.…
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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
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