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93 results • Page
2 of 2
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Replies
0
votes
0
replies
7
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
20 minutes ago by
Aaliya
▴ 10
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
178
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
195
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 6 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
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
1
vote
0
replies
538
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
5 days ago by
mathavanbioinfo
▴ 90
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
0
replies
125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 3 days ago by
Carlo Yague
8.7k • written 4 days ago by
Atul K.
• 0
0
votes
0
replies
79
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
3 days ago by
Biostars2200
• 0
0
votes
0
replies
72
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
0
votes
0
replies
89
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
0
votes
0
replies
70
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
0
votes
0
replies
79
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
0
votes
0
replies
82
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
0
votes
0
replies
84
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
0
votes
0
replies
90
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
194
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 3 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
0
replies
106
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
75
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
0
votes
0
replies
86
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 2 days ago by
SHREYA
• 0
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
0
replies
92
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
0
replies
83
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
0
replies
103
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
0
replies
124
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
0
votes
0
replies
240
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
0
replies
119
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 1 day ago by
Jeyong
• 0
0
votes
0
replies
95
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
0
replies
72
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
20 hours ago by
Aspire
▴ 300
0
votes
0
replies
57
views
how to read graph_test output of monocle 3
monocle3
13 hours ago by
synat.keam
▴ 100
93 results • Page
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Recent Votes
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
Answer: Missing protein (VEGF-A) in String db
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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.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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