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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.5 years ago by
anonymous1192976466
▴ 50
12
votes
8
replies
1.3k
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 19 months ago by
Matthias Zepper
4.5k • written 19 months ago by
A_heath
▴ 160
12
votes
11
replies
3.2k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.7 years ago by
Lars Juhl Jensen
11k • written 13.0 years ago by
Pri
▴ 20
12
votes
12
replies
4.9k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 10.4 years ago by
Istvan Albert
100k • written 10.4 years ago by
biolab
★ 1.4k
12
votes
8
replies
3.2k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
7.3 years ago by
statfa
▴ 760
12
votes
14
replies
5.7k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.2 years ago by
star
▴ 350
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.3 years ago by
John
13k
12
votes
13
replies
2.7k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 16 months ago by
Ram
43k • written 8.8 years ago by
sarathkurichiyil
• 0
12
votes
21
replies
3.2k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
Miguel
▴ 30
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 16 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
1.4k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
3.8 years ago by
screadore
▴ 20
11
votes
2
replies
1.5k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
4.7 years ago by
WUSCHEL
▴ 750
11
votes
29
replies
9.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
11
votes
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.9 years ago by
plebaninora
• 0
11
votes
6
replies
3.2k
views
Understanding Supplementary reads.
Bowtie2
MEM
BWA
Dragen
updated 2.2 years ago by
Istvan Albert
100k • written 2.2 years ago by
kiran
▴ 10
11
votes
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 16 months ago by
Ram
43k • written 8.9 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
10
replies
5.8k
views
Best mapping software to generate BAM file
BAM
mapping
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
Anand Rao
▴ 630
11
votes
24
replies
5.4k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 510
11
votes
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
7.5 years ago by
CF
▴ 50
11
votes
5
replies
1.3k
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 2.4 years ago by
ATpoint
82k • written 2.4 years ago by
suzanne rein
▴ 10
11
votes
11
replies
2.7k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 8.0 years ago by
Biostar
20 • written 8.0 years ago by
12021560-040
▴ 70
11
votes
3
replies
954
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
13 months ago by
DareDevil
★ 4.3k
11
votes
6
replies
6.3k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.8 years ago by
Jokhe
▴ 140
11
votes
10
replies
1.6k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 7.6 years ago by
Biostar
20 • written 7.6 years ago by
Farbod
★ 3.4k
11
votes
15
replies
2.8k
views
How do I get the read counts for a specific exon
bam
exon
updated 6.1 years ago by
Ram
43k • written 6.1 years ago by
b10hazard
▴ 30
11
votes
11
replies
5.6k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
6.2 years ago by
ishackm
▴ 110
11
votes
4
replies
2.6k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 7.8 years ago by
Biostar
20 • written 8.0 years ago by
William
★ 5.3k
11
votes
11
replies
1.0k
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
4.0 years ago by
lokeshp14cs24
• 0
10
votes
8
replies
6.1k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.6 years ago by
Neilfws
49k • written 12.6 years ago by
Liyf
▴ 300
10
votes
7
replies
1.2k
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
6.0 years ago by
mhyunjunkang
▴ 110
10
votes
3
replies
1.4k
views
how to create new file
r
updated 7.5 years ago by
GenoMax
141k • written 7.5 years ago by
forever
▴ 80
10
votes
25
replies
3.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.2 years ago by
Biostar
20 • written 7.4 years ago by
mra8187
▴ 20
10
votes
8
replies
2.3k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 22 months ago by
Ram
43k • written 9.1 years ago by
friasoler
▴ 50
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
10
votes
8
replies
1.7k
views
File Format - Fasta
sequence
8.1 years ago by
Gabe Anderson
▴ 10
10
votes
15
replies
6.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 13 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
10
votes
1
reply
4.0k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 10.4 years ago by
Biostar
20 • written 11.1 years ago by
Ashutosh Pandey
12k
10
votes
6
replies
975
views
RNA seq, secreted protein
protein
gene
secreted
updated 8 months ago by
Joe
21k • written 16 months ago by
Rob
▴ 170
10
votes
11
replies
4.7k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
10.2 years ago by
inadamj
▴ 60
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.4 years ago by
Farbod
★ 3.4k
10
votes
11
replies
9.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
SheelS
▴ 40
10
votes
11
replies
1.6k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
5.4 years ago by
Chaimaa
▴ 260
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.2 years ago by
XBria
▴ 90
10
votes
19
replies
3.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.9 years ago by
GenoMax
141k • written 3.0 years ago by
matt
▴ 20
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
3.3 years ago by
DareDevil
★ 4.3k
10
votes
2
replies
598
views
any script that can do this task
shell-script
updated 2.1 years ago by
Ram
43k • written 2.1 years ago by
Confused_human
▴ 20
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
10 months ago by
Chris
▴ 260
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 10 months ago by
Ram
43k • written 4.2 years ago by
gable_works
▴ 50
1,000 results • Page
2 of 20
Recent Votes
Comment: Sequence read length shorter than flow cell specification
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
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Recent Replies
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/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : ```r 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
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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
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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…
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