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1,000 results • Page
2 of 20
Sort: Votes
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Votes
Replies
12
votes
17
replies
3.8k
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
5.4 years ago by
anonymous1192976466
▴ 50
12
votes
10
replies
2.3k
views
7 follow
SAM / BAM alignments
SAM
BAM
6.2 years ago by
John
13k
11
votes
22
replies
2.8k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
3.9 years ago by
RNAseqer
▴ 220
11
votes
10
replies
9.8k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 15 months ago by
Ram
38k • written 8.6 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
984
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
2.7 years ago by
screadore
▴ 20
11
votes
2
replies
1.3k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
3.6 years ago by
WUSCHEL
▴ 720
11
votes
6
replies
3.1k
views
bcftools isec -n operators
bcftools
intersect
updated 19 months ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
11
votes
11
replies
4.7k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
5.1 years ago by
ishackm
▴ 110
11
votes
5
replies
863
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 15 months ago by
ATpoint
70k • written 15 months ago by
suzanne rein
▴ 10
11
votes
11
replies
2.3k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 6.9 years ago by
Biostar
20 • written 6.9 years ago by
12021560-040
▴ 70
11
votes
7
replies
2.9k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
6.4 years ago by
CF
▴ 50
11
votes
10
replies
5.0k
views
Best mapping software to generate BAM file
BAM
mapping
updated 5.3 years ago by
Biostar
20 • written 5.5 years ago by
Anand Rao
▴ 550
11
votes
29
replies
8.0k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 17 months ago by
Ram
38k • written 8.8 years ago by
Parham
★ 1.6k
11
votes
15
replies
2.3k
views
How do I get the read counts for a specific exon
bam
exon
updated 5.0 years ago by
Ram
38k • written 5.0 years ago by
b10hazard
▴ 30
11
votes
6
replies
5.5k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
5.7 years ago by
Jokhe
▴ 130
11
votes
10
replies
2.3k
views
6 follow
Genomic statistics from gtf
gene
gtf
4.8 years ago by
plebaninora
• 0
11
votes
4
replies
2.3k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
William
★ 5.2k
11
votes
10
replies
1.2k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 6.5 years ago by
Biostar
20 • written 6.5 years ago by
Farbod
★ 3.4k
11
votes
9
replies
2.1k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 12 weeks ago by
Ram
38k • written 7.8 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
11
replies
621
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
2.9 years ago by
lokeshp14cs24
• 0
11
votes
24
replies
3.9k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
3.9 years ago by
williamsbrian5064
▴ 470
10
votes
8
replies
5.7k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 11.5 years ago by
Neilfws
49k • written 11.5 years ago by
Liyf
▴ 300
10
votes
19
replies
2.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 22 months ago by
GenoMax
127k • written 22 months ago by
matt
▴ 20
10
votes
5
replies
5.1k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 9.1 years ago by
Biostar
20 • written 11.9 years ago by
Arun
2.4k
10
votes
25
replies
2.6k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
Za
▴ 140
10
votes
4
replies
990
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
2.2 years ago by
dare_devil
★ 1.7k
10
votes
10
replies
1.6k
views
Minor allele frequency
GWAS
SNPs
Alleles
updated 4.4 years ago by
Biostar
20 • written 6.3 years ago by
alessandrotestori7
▴ 410
10
votes
12
replies
1.5k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
4.1 years ago by
msimmer92
▴ 300
10
votes
9
replies
1.6k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
4.8 years ago by
Angelique
▴ 10
10
votes
8
replies
1.9k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 9 months ago by
Ram
38k • written 8.0 years ago by
friasoler
▴ 30
10
votes
2
replies
347
views
any script that can do this task
shell-script
updated 12 months ago by
Ram
38k • written 12 months ago by
adyashapanda04
▴ 10
10
votes
11
replies
4.1k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
9.1 years ago by
inadamj
▴ 60
10
votes
2
replies
2.6k
views
Standalone Blast Issue
blast
10.8 years ago by
chlazaris
• 0
10
votes
13
replies
5.1k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
6.1 years ago by
Vasu
▴ 720
10
votes
11
replies
1.2k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
4.3 years ago by
Chaimaa
▴ 260
10
votes
23
replies
1.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.3 years ago by
GenoMax
127k • written 5.3 years ago by
Farbod
★ 3.4k
10
votes
10
replies
3.2k
views
Parameter optimization STAR
RNA-Seq
5.1 years ago by
XBria
▴ 90
10
votes
5
replies
2.2k
views
error with samtools
RNA-Seq
updated 6.1 years ago by
Biostar
20 • written 6.3 years ago by
mra8187
▴ 20
10
votes
1
reply
3.7k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 9.3 years ago by
Biostar
20 • written 10.0 years ago by
Ashutosh Pandey
12k
10
votes
11
replies
5.4k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.4 years ago by
jackgrayner
▴ 50
10
votes
7
replies
944
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
4.9 years ago by
mhyunjunkang
▴ 110
10
votes
11
replies
8.2k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 9 months ago by
Ram
38k • written 8.0 years ago by
SheelS
▴ 40
10
votes
8
replies
1.5k
views
File Format - Fasta
sequence
7.0 years ago by
Gabe Anderson
▴ 10
10
votes
21
replies
2.3k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.6 years ago by
Biostar
20 • written 3.7 years ago by
Miguel
▴ 10
10
votes
14
replies
3.6k
views
ATAC-seq data and deepTools: Small detail with impact on output
deeptools
ATACseq
bigwig
readlength
Forum
updated 3.1 years ago by
ATpoint
70k • written 3.1 years ago by
gable_works
▴ 50
10
votes
7
replies
912
views
Can two mates have different file size?
sequencing
fastq
4.6 years ago by
marongiu.luigi
▴ 670
10
votes
5
replies
6.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 7 months ago by
Ram
38k • written 7.6 years ago by
seta
★ 1.8k
10
votes
6
replies
2.5k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 10 hours ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
10
votes
7
replies
3.2k
views
What is Pathway Analysis?
pathway
analysis
ontology
database
tools
6.9 years ago by
Pranavathiyani G
▴ 330
10
votes
15
replies
5.1k
views
convert fasta/gb to vcf
vcf
reference
file conversion
4.5 years ago by
marongiu.luigi
▴ 670
1,000 results • Page
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Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Ruben
• 0
> Unfortunately, as far as I can tell, WDL provides no support for iterating over the contents of a directory. (I find this shocking. I con…
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial suppli…
Comment: RNA-SEQ
by
ali
• 0
thanks for your helping
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
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iraun
5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
Andy
• 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39
by
seidel
11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard
by
ntsopoul
▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
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rheab1230
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Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks
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rheab1230
▴ 140
thank you. i will go through it
Comment: Fastqc report analysis
by
npavliukovec
• 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number
by
kimgeng
• 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number
by
ntsopoul
▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
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by
ntsopoul
▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
Comment: Easy way to split VCF file by chromosome
by
Joana
• 0
You need to run bcftools index on your vcf file before running the suggested command.
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