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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
12
votes
10
replies
2.6k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.7 years ago by
John
13k
12
votes
17
replies
4.2k
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
6.0 years ago by
anonymous1192976466
▴ 50
12
votes
28
replies
2.2k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.3 years ago by
Za
▴ 140
12
votes
8
replies
892
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 12 months ago by
Matthias Zepper
4.1k • written 12 months ago by
A_heath
▴ 140
11
votes
22
replies
3.4k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.4 years ago by
RNAseqer
▴ 250
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 21 months ago by
Ram
40k • written 9.1 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
1.2k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
3.3 years ago by
screadore
▴ 20
11
votes
2
replies
1.4k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
4.1 years ago by
WUSCHEL
▴ 720
11
votes
11
replies
2.5k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 7.4 years ago by
Biostar
20 • written 7.4 years ago by
12021560-040
▴ 70
11
votes
11
replies
797
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
3.4 years ago by
lokeshp14cs24
• 0
11
votes
29
replies
8.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 23 months ago by
Ram
40k • written 9.3 years ago by
Parham
★ 1.6k
11
votes
11
replies
5.1k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
5.6 years ago by
ishackm
▴ 110
11
votes
4
replies
2.5k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
William
★ 5.2k
11
votes
15
replies
2.5k
views
How do I get the read counts for a specific exon
bam
exon
updated 5.5 years ago by
Ram
40k • written 5.5 years ago by
b10hazard
▴ 30
11
votes
6
replies
5.9k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.2 years ago by
Jokhe
▴ 130
11
votes
24
replies
4.7k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.4 years ago by
williamsbrian5064
▴ 480
11
votes
10
replies
1.4k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 7.0 years ago by
Biostar
20 • written 7.0 years ago by
Farbod
★ 3.4k
11
votes
6
replies
3.6k
views
bcftools isec -n operators
bcftools
intersect
updated 2.1 years ago by
Ram
40k • written 3.7 years ago by
Begonia_pavonina
▴ 100
11
votes
10
replies
5.4k
views
Best mapping software to generate BAM file
BAM
mapping
updated 5.8 years ago by
Biostar
20 • written 6.0 years ago by
Anand Rao
▴ 570
11
votes
5
replies
1.1k
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 22 months ago by
ATpoint
77k • written 22 months ago by
suzanne rein
▴ 10
11
votes
10
replies
2.6k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.3 years ago by
plebaninora
• 0
11
votes
9
replies
2.3k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 9 months ago by
Ram
40k • written 8.3 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
7
replies
3.1k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
6.9 years ago by
CF
▴ 50
10
votes
8
replies
5.8k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.1 years ago by
Neilfws
49k • written 12.1 years ago by
Liyf
▴ 300
10
votes
5
replies
2.3k
views
error with samtools
RNA-Seq
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
mra8187
▴ 20
10
votes
8
replies
2.1k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 15 months ago by
Ram
40k • written 8.5 years ago by
friasoler
▴ 30
10
votes
23
replies
2.0k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.9 years ago by
GenoMax
134k • written 5.9 years ago by
Farbod
★ 3.4k
10
votes
14
replies
4.3k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 3 months ago by
Ram
40k • written 3.6 years ago by
gable_works
▴ 50
10
votes
19
replies
2.8k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.4 years ago by
GenoMax
134k • written 2.4 years ago by
matt
▴ 20
10
votes
11
replies
1.4k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
4.8 years ago by
Chaimaa
▴ 260
10
votes
7
replies
1.1k
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
5.4 years ago by
mhyunjunkang
▴ 110
10
votes
6
replies
691
views
RNA seq, secreted protein
protein
gene
secreted
updated 7 weeks ago by
Joe
21k • written 9 months ago by
Rob
▴ 160
10
votes
11
replies
8.6k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 16 months ago by
Ram
40k • written 8.5 years ago by
SheelS
▴ 40
10
votes
4
replies
1.2k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
2.7 years ago by
DareDevil
★ 3.3k
10
votes
5
replies
5.3k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 9.7 years ago by
Biostar
20 • written 12.4 years ago by
Arun
2.4k
10
votes
10
replies
1.7k
views
Minor allele frequency
GWAS
SNPs
Alleles
updated 4.9 years ago by
Biostar
20 • written 6.8 years ago by
alessandrotestori7
▴ 410
10
votes
2
replies
450
views
any script that can do this task
shell-script
updated 18 months ago by
Ram
40k • written 18 months ago by
Confused_human
▴ 10
10
votes
5
replies
6.8k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 13 months ago by
Ram
40k • written 8.1 years ago by
seta
★ 1.8k
10
votes
15
replies
5.8k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
6.8 years ago by
Farbod
★ 3.4k
10
votes
15
replies
5.6k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 6 months ago by
Ram
40k • written 5.0 years ago by
marongiu.luigi
▴ 690
10
votes
1
reply
3.8k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 9.9 years ago by
Biostar
20 • written 10.6 years ago by
Ashutosh Pandey
12k
10
votes
1
reply
3.3k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 13 months ago by
Ram
40k • written 8.3 years ago by
Niek De Klein
★ 2.6k
10
votes
7
replies
1.0k
views
Can two mates have different file size?
sequencing
fastq
5.1 years ago by
marongiu.luigi
▴ 690
10
votes
2
replies
2.7k
views
Standalone Blast Issue
blast
11.3 years ago by
chlazaris
• 0
10
votes
6
replies
2.7k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 6 months ago by
Ram
40k • written 8.3 years ago by
lait
▴ 180
10
votes
13
replies
5.4k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
6.6 years ago by
Vasu
▴ 730
10
votes
3
replies
1.3k
views
how to create new file
r
updated 6.9 years ago by
GenoMax
134k • written 6.9 years ago by
forever
▴ 80
10
votes
9
replies
1.7k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
5.4 years ago by
Angelique
▴ 10
10
votes
21
replies
2.7k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.1 years ago by
Biostar
20 • written 4.2 years ago by
Miguel
▴ 10
10
votes
12
replies
1.7k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
4.6 years ago by
msimmer92
▴ 300
1,000 results • Page
2 of 20
Recent Votes
Comment: module and trait correlation for WGCNA
Peak annotation with HOMER. Statistics with the annStats parameter
Answer: Fetch Fastq files directly for SRA data
Answer: Fetch Fastq files directly for SRA data
A: Using TargetScan on other species
Comment: Low Alignment rate
Comment: ncbi error report log for validate fastq issue
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Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
GenoMax
134k
This may be one of those things that just happens to be a one-time thing with whatever was going on with this run. Was this sample pooled w…
Comment: ncbi error report log for validate fastq issue
by
GenoMax
134k
Can you provide details of what you are doing and the commands you are using?
Comment: Fetch Fastq files directly for SRA data
by
GenoMax
134k
> fetch fastq files for SRA data hosted by NCBI from AWS data exchange Please provide an example of a SRA accession where you are encount…
Comment: How the first sequencing template removed in pair end sequencing
by
GenoMax
134k
Moving this to an answer since there is a link for a paper. Things could have changed as @rfran010 says but this may be the closest we will…
Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
Asaf
10k
What machine? (Nextseq? Novaseq?) what library prep method?
Comment: How to determine the total count for each gene in lymphotype B
by
fracarb8
★ 1.2k
If you want the average expression, you should look at `AverageExpression` from seurat which returns the average instead of the sum. `Avera…
Answer: Fetch Fastq files directly for SRA data
by
Umer
▴ 50
You can also use **[Grabseqs][1]**. Easiest way is to use it with anaconda as **conda install -c louiejtaylor grabseqs** But you have…
Answer: chromosome location
by
Umer
▴ 50
What you can do is use **SnapGene** 1. Download the genome (fasta file) 2. Load it into Snapgene 3. Find gene locations based on the …
Comment: Troubles launch IGV on Linux(Debian)
by
barslmn
★ 1.8k
Your log seems fine. Could you add the results of these commands? - Which version of debian are you on? ``` lsb_release -c `…
Comment: How to plot coverage and depth statistics of a bam file
by
jl19
• 0
Hi William, I was trying to use bam2plot you have developed. It was installed on a python evnviroment python version 3.11. The installat…
Comment: Help writing code for a question on my homework
by
Joe
21k
This isn't really the right place for this question. Please ask this as a separate new question, but only if it is bioinformatics related.
Comment: How to determine the total count for each gene in lymphotype B
by
dalibenam64
• 0
thank you very much for your response I'm really grateful !! but I'm still confused because for example for patients I have 2 replicates…
Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
eggrandio
▴ 40
But shouldn't quality drop at both 3'ends and not just on the left one?
Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
ATpoint
77k
https://www.biostars.org/p/91624/
Comment: to annotate BEDPE files
by
Lhl
▴ 760
is this what you are looking for? https://github.com/imgag/ngs-bits/blob/master/doc/tools/BedpeGeneAnnotation.md
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