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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
3
replies
188
views
from row count to tpm
tpm
row-count
normalization
2 days ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
253
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
2
votes
3
replies
311
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 3 days ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
0
votes
1
reply
124
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
2
replies
188
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
3
votes
3
replies
207
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Mariana
▴ 10
0
votes
1
reply
119
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
0
replies
82
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
3
votes
3
replies
712
views
KissDE and batch effect
kissDE
kissplice
3 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
74
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
19 hours ago by
Kevin Blighe
87k
0
votes
0
replies
80
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
2
votes
4
replies
252
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 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
80
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
121
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
3 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
280
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
1 day ago by
HyperEvo
• 0
0
votes
1
reply
147
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
2
replies
187
views
Result of running of p3_in.pl
primer3
updated 3 days ago by
GenoMax
141k • written 3 days ago by
nasri
• 0
0
votes
1
reply
128
views
FAM FILE
file
Fam
3 days ago by
Eleonora
• 0
0
votes
0
replies
70
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
3
votes
5
replies
252
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 3 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
88
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
3
votes
5
replies
538
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
3 days ago by
n_navy
• 0
0
votes
0
replies
72
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
6
votes
3
replies
170
views
Interpretting IGV output
IGV
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
analyst
▴ 30
0
votes
1
reply
174
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
Ayush
• 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
1
vote
5
replies
307
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
2 days ago by
anasjamshed
▴ 120
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 3 days ago by
Atul K.
• 0
3
votes
2
replies
266
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
3 days ago by
kristiewyleung
• 0
2
votes
5
replies
441
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
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 4 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
4 days ago by
Mamatha Y S
• 0
0
votes
0
replies
129
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 4 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
518
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 days ago by
ATpoint
82k • written 6 days ago by
rheab1230
▴ 140
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
7
votes
6
replies
460
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
4 days ago by
analyst
▴ 30
1
vote
1
reply
254
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Bioinformatician
• 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
1
vote
1
reply
296
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 5 days ago by
Ram
43k • written 5 days ago by
Nina
• 0
2
votes
5
replies
516
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Giorgio
• 0
2
votes
1
reply
284
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 5 days ago by
GenoMax
141k • written 6 days ago by
rebecca.calvo
• 0
0
votes
0
replies
211
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
2
votes
5
replies
681
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
Ann
★ 2.4k
0
votes
0
replies
186
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
0
replies
187
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
6 days ago by
Nitin
• 0
1
vote
5
replies
555
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Luka
• 0
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Ram
43k • written 6 days ago by
yifangt86
▴ 60
1,000 results • Page
3 of 20
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
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/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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