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94 results • Page
2 of 2
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Votes
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0
votes
5
replies
285
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
0
votes
0
replies
243
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
1 day ago by
pramach1
▴ 40
0
votes
1
reply
138
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
0
replies
122
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
110
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
0
votes
0
replies
93
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
2
replies
234
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
0
votes
0
replies
100
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
0
votes
4
replies
248
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
23 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
76
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
23 hours ago by
Aspire
▴ 300
0
votes
5
replies
279
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 18 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
1
reply
154
views
PCA plot
DESeq2
PCAplot
updated 17 hours ago by
jkim
▴ 170 • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
389
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 17 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
60
views
how to read graph_test output of monocle 3
monocle3
16 hours ago by
synat.keam
▴ 100
0
votes
0
replies
56
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
15 hours ago by
Emily
▴ 10
0
votes
0
replies
65
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
15 hours ago by
avocado123
• 0
0
votes
1
reply
94
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 12 hours ago by
ATpoint
82k • written 12 hours ago by
AaronJaime
• 0
0
votes
2
replies
154
views
Highest variable features in single cell data
single-cell
updated 11 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
202
views
Annovar using R package
Annovar
gnomAD
R
11 hours ago by
DKA
▴ 40
0
votes
0
replies
52
views
Designing single-stable RNA molecules
structure
RNA
11 hours ago by
Edna
• 0
0
votes
0
replies
62
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
11 hours ago by
simplitia
▴ 130
0
votes
11
replies
456
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
8 hours ago by
atowns21
• 0
0
votes
0
replies
31
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
4 hours ago by
turcoa1
• 0
0
votes
0
replies
15
views
RNA-seq: full length gene
identification
gene
full
length
2 hours ago by
Nargis
• 0
0
votes
0
replies
20
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
1 hour ago by
SineWave
• 0
0
votes
0
replies
15
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
1 hour ago by
KABILAN
▴ 40
0
votes
3
replies
91
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 20 minutes ago by
Pierre Lindenbaum
161k • written 3 hours ago by
J
• 0
0
votes
0
replies
194
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by
Atul K.
• 0
0
votes
0
replies
31
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 20 minutes ago by
Pierre Lindenbaum
161k • written 3 hours ago by
Aaliya
▴ 10
0
votes
0
replies
178
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
0
votes
1
reply
281
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by
Ram
43k • written 6 days ago by
Kazo
• 0
0
votes
0
replies
196
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 6 days ago by
Ram
43k • written 6 days ago by
Dinmukhamed
• 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by
Ram
43k • written 7 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
204
views
Copy number variation plot
Copy-number-variation
genomics
updated 6 days ago by
Ram
43k • written 6 days ago by
Emmi
• 0
0
votes
0
replies
181
views
Chemical structure validation
structure
cap
validation
metabolite
6 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
261
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 6 days ago by
GenoMax
141k • written 6 days ago by
bioyas
▴ 10
0
votes
0
replies
188
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Ram
43k • written 6 days ago by
yifangt86
▴ 60
0
votes
0
replies
188
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
6 days ago by
Nitin
• 0
0
votes
0
replies
187
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 6 days ago by
Ram
43k • written 6 days ago by
mja
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 5 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
0
replies
212
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
5 days ago by
abhishekghadge
• 0
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
5 days ago by
Mamatha Y S
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
5 days ago by
rthapa
▴ 90
94 results • Page
2 of 2
Recent Votes
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis
by
LauferVA
4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
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