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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
6.6 years ago by
anonymous1192976466
▴ 50
12
votes
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.3 years ago by
star
▴ 350
12
votes
8
replies
1.3k
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 20 months ago by
Matthias Zepper
4.6k • written 20 months ago by
A_heath
▴ 160
12
votes
10
replies
3.0k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.4 years ago by
John
13k
12
votes
11
replies
3.3k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.7 years ago by
Lars Juhl Jensen
11k • written 13.1 years ago by
Pri
▴ 20
12
votes
10
replies
4.2k
views
Speed up BLASTp vs NCBI nr database
blast
8.0 years ago by
biotech
▴ 570
12
votes
21
replies
3.3k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
Miguel
▴ 30
12
votes
28
replies
2.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
6.0 years ago by
Za
▴ 140
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
12
replies
5.0k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 10.5 years ago by
Istvan Albert
100k • written 10.5 years ago by
biolab
★ 1.4k
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 6 weeks ago by
Ram
44k • written 5.1 years ago by
RNAseqer
▴ 270
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.4 years ago by
Ram
44k • written 9.8 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
3.9 years ago by
screadore
▴ 20
11
votes
2
replies
1.5k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
4.8 years ago by
WUSCHEL
▴ 760
11
votes
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 17 months ago by
Ram
44k • written 9.0 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
24
replies
5.6k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.1 years ago by
williamsbrian5064
▴ 520
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 7.9 years ago by
Biostar
20 • written 8.1 years ago by
William
★ 5.3k
11
votes
6
replies
6.4k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.9 years ago by
Jokhe
▴ 140
11
votes
3
replies
1.0k
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
14 months ago by
DareDevil
★ 4.3k
11
votes
10
replies
1.7k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 7.7 years ago by
Biostar
20 • written 7.7 years ago by
Farbod
★ 3.4k
11
votes
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
7.5 years ago by
CF
▴ 50
11
votes
29
replies
10.0k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.6 years ago by
Ram
44k • written 10.0 years ago by
Parham
★ 1.6k
11
votes
11
replies
2.8k
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
10
replies
5.8k
views
Best mapping software to generate BAM file
BAM
mapping
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
Anand Rao
▴ 630
11
votes
5
replies
1.4k
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 2.5 years ago by
ATpoint
82k • written 2.5 years ago by
suzanne rein
▴ 10
11
votes
11
replies
1.1k
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
4.1 years ago by
lokeshp14cs24
• 0
11
votes
6
replies
3.3k
views
Understanding Supplementary reads.
Bowtie2
MEM
BWA
Dragen
updated 2.3 years ago by
Istvan Albert
100k • written 2.3 years ago by
kiran
▴ 10
11
votes
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
6.0 years ago by
plebaninora
• 0
11
votes
15
replies
2.9k
views
How do I get the read counts for a specific exon
bam
exon
updated 6.2 years ago by
Ram
44k • written 6.2 years ago by
b10hazard
▴ 30
11
votes
11
replies
5.7k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
6.2 years ago by
ishackm
▴ 110
10
votes
8
replies
6.1k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.7 years ago by
Neilfws
49k • written 12.7 years ago by
Liyf
▴ 300
10
votes
12
replies
2.0k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
5.3 years ago by
msimmer92
▴ 300
10
votes
7
replies
1.3k
views
Can two mates have different file size?
sequencing
fastq
5.8 years ago by
marongiu.luigi
▴ 710
10
votes
9
replies
2.0k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
6.0 years ago by
Angelique
▴ 10
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.5 years ago by
Farbod
★ 3.4k
10
votes
13
replies
5.8k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
7.2 years ago by
Vasu
▴ 770
10
votes
19
replies
3.5k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
matt
▴ 20
10
votes
3
replies
1.4k
views
how to create new file
r
updated 7.5 years ago by
GenoMax
142k • written 7.5 years ago by
forever
▴ 80
10
votes
1
reply
4.0k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 10.5 years ago by
Biostar
20 • written 11.2 years ago by
Ashutosh Pandey
12k
10
votes
8
replies
1.8k
views
File Format - Fasta
sequence
8.2 years ago by
Gabe Anderson
▴ 10
10
votes
10
replies
3.9k
views
Parameter optimization STAR
RNA-Seq
6.3 years ago by
XBria
▴ 90
10
votes
23
replies
2.5k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 6.5 years ago by
GenoMax
142k • written 6.5 years ago by
Farbod
★ 3.4k
10
votes
6
replies
8.5k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.9 years ago by
alserg
▴ 930 • written 2.9 years ago by
gabrielbaldanzi
▴ 10
10
votes
14
replies
5.1k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 11 months ago by
Ram
44k • written 4.3 years ago by
gable_works
▴ 50
10
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by
yoshifumimiya
▴ 50
10
votes
11
replies
4.7k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
10.3 years ago by
inadamj
▴ 60
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
3.4 years ago by
DareDevil
★ 4.3k
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
7
replies
1.2k
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
6.1 years ago by
mhyunjunkang
▴ 110
10
votes
5
replies
7.4k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 21 months ago by
Ram
44k • written 8.7 years ago by
seta
★ 1.9k
1,000 results • Page
2 of 20
Recent Votes
Answer: Cut&Run and heatmap
Comment: Functional enrichment analysis for unique gene IDs
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
How do i calculate the mean of triplicates in a data.frame based on pattern?
C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
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Comment: txt file to bigwig
by
ATpoint
82k
Please stop asking questions in existing threads. Delete these two comments and open a new question with all the necessary details to under…
Comment: Venter Genome Vcf
by
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22k
there are some violations in this VCF: - Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=St…
Comment: Cut&Run and heatmap
by
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Hi all, I am new to cut&run or any peak-related analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt …
Comment: Functional enrichment analysis for unique gene IDs
by
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▴ 100
Since the locus-tags are unclassified, I used the CDS instead of the locus-tags to retrive their ensembl IDs using ensembl bacteria website…
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by
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Could you find a solution to your problem?
Comment: txt file to bigwig
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sogand
• 0
Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
Answer: Help me with Heatmap
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Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
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1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
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mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
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142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
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It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
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In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
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Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
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wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
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by
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I'm a happy user of [data.table](https://rdatatable.gitlab.io/data.table/): ``` library(data.table) dat <- structure(list(sgrna = c("Cont…
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