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94 results • Page
2 of 2
Sort: Votes
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Votes
Replies
0
votes
0
replies
247
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
139
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
129
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
112
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 2 days ago by
newuser2024
• 0
0
votes
0
replies
94
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
103
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
249
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
80
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
5
replies
284
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
1
reply
394
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 20 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
63
views
how to read graph_test output of monocle 3
monocle3
19 hours ago by
synat.keam
▴ 100
0
votes
0
replies
61
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
18 hours ago by
Emily
▴ 10
0
votes
0
replies
70
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
18 hours ago by
avocado123
• 0
0
votes
1
reply
103
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 15 hours ago by
ATpoint
82k • written 15 hours ago by
AaronJaime
• 0
0
votes
2
replies
158
views
Highest variable features in single cell data
single-cell
updated 14 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
207
views
Annovar using R package
Annovar
gnomAD
R
14 hours ago by
DKA
▴ 40
0
votes
0
replies
57
views
Designing single-stable RNA molecules
structure
RNA
14 hours ago by
Edna
• 0
0
votes
0
replies
66
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
13 hours ago by
simplitia
▴ 130
0
votes
11
replies
462
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
11 hours ago by
atowns21
• 0
0
votes
0
replies
34
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
7 hours ago by
turcoa1
• 0
0
votes
0
replies
35
views
RNA-seq: full length gene
identification
gene
full
length
5 hours ago by
Nargis
• 0
0
votes
0
replies
38
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
4 hours ago by
SineWave
• 0
0
votes
3
replies
150
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 3 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
J
• 0
0
votes
1
reply
40
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 hours ago by
Joe
21k • written 2 hours ago by
sapuizait
▴ 10
0
votes
0
replies
26
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 hours ago by
HarperReed
• 0
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
175
views
PCA plot
DESeq2
PCAplot
updated 2 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
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
282
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 6 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
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 4 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
2
replies
258
views
bam merging for archaic samples
samtools
bam
updated 4 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
94 results • Page
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Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Recent Replies
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Answer: Rare Disease Variant Pathway Analysis
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The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt
by
Joe
21k
If you have the accession numbers can you not use something like `eutils`?
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…
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