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525 results • Page
2 of 11
Sort: Votes
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Views
Votes
Replies
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
2
votes
0
replies
203
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
10 days ago by
Alexander
▴ 220
2
votes
6
replies
630
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 23 days ago by
Ram
43k • written 4 months ago by
zea
• 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 16 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 8 days ago by
Ram
43k • written 3.4 years ago by
chatterjee.arumoy
▴ 50
2
votes
10
replies
822
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 28 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 24 days ago by
andorjkiss
▴ 40 • written 15 months ago by
javanokendo
▴ 60
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 20 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
2
votes
7
replies
812
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
2
votes
6
replies
399
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
17 days ago by
jkim
▴ 170
2
votes
4
replies
252
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 10
2
votes
2
replies
264
views
singlecell annotation
scRNA-seq
annotation
29 days ago by
kayah
• 0
2
votes
4
replies
315
views
SnpEff annotates coding duplication as intronic?
snpeff
8 days ago by
kirill.zaslavsky
• 0
2
votes
3
replies
254
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 23 days ago by
Ram
43k • written 23 days ago by
Netanel
• 0
2
votes
3
replies
928
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 10 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
2
votes
9
replies
814
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
2
replies
259
views
Removing adapters in all the RNAseq samples regardless if they have or not, is it correct?
fastqc
trimming
adapters
cutadapt
RNAseq
updated 21 days ago by
dsull
★ 5.8k • written 22 days ago by
ev97
▴ 20
1
vote
4
replies
388
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 12 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
Morteza
• 0
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
1
vote
2
replies
229
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 17 days ago by
Netanel
• 0
1
vote
2
replies
271
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
Ram
43k • written 8 days ago by
aniigodwinn
• 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 8 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
0
replies
149
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 28 days ago by
Ram
43k • written 28 days ago by
Tolga
▴ 30
1
vote
3
replies
199
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
1
vote
2
replies
208
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 28 days ago by
Ram
43k • written 28 days ago by
gdfsnkfns
• 0
1
vote
1
reply
175
views
Failed to download data from EBI with ascp
EBI
aspera
updated 14 days ago by
GenoMax
141k • written 14 days ago by
biock
▴ 60
1
vote
0
replies
47
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
5 hours ago by
rohitsatyam102
▴ 850
1
vote
3
replies
349
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 24 days ago by
Pierre Lindenbaum
161k • written 25 days ago by
Max
• 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 8 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
1
vote
1
reply
820
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 20 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
1
vote
2
replies
287
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
9 days ago by
bp22
▴ 80
1
vote
1
reply
462
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 17 days ago by
chrchang523
10k • written 17 days ago by
dsbusiness135
▴ 10
1
vote
1
reply
190
views
Tool for gene function identification
Gene-Function
updated 23 days ago by
Ram
43k • written 23 days ago by
Estevão
• 0
1
vote
3
replies
237
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
1
vote
4
replies
812
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
15 days ago by
Hyper_Odin
▴ 310
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 23 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
1
vote
1
reply
223
views
Retrieve a % coverage for each transcript
RNA-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
jammydodger123456
▴ 40
1
vote
2
replies
626
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
27 days ago by
colindaven
6.4k
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 10 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
1
vote
2
replies
327
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 22 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
1
vote
2
replies
314
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 10 days ago by
Istvan Albert
100k • written 11 days ago by
Jiang
• 0
1
vote
3
replies
253
views
CCA with random effects model
CCA
updated 23 days ago by
dariober
14k • written 23 days ago by
leranwangcs
▴ 120
1
vote
0
replies
368
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 16 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
0
replies
155
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 14 days ago by
Ram
43k • written 14 days ago by
ian.will
▴ 30
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
9 days ago by
bioinfo
▴ 150
1
vote
3
replies
345
views
Ensembl gene id conversion
biomart
ensembl
updated 9 days ago by
ATpoint
82k • written 11 days ago by
naveedhasan2000
• 0
1
vote
2
replies
922
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 20 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
525 results • Page
2 of 11
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
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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
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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
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▴ 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
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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
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161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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