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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
12
votes
10
replies
4.1k
views
Speed up BLASTp vs NCBI nr database
blast
8.0 years ago by
biotech
▴ 570
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
28
replies
2.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.4 years ago by
John
13k
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
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
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 4.8 years ago by
Miguel
▴ 30
12
votes
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.2 years ago by
star
▴ 350
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
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
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 5 weeks ago by
Ram
43k • 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
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
3.9 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
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 7.7 years ago by
Farbod
★ 3.4k
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
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 17 months ago by
Ram
43k • written 8.9 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
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
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.9 years ago by
plebaninora
• 0
11
votes
6
replies
6.3k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.9 years ago by
Jokhe
▴ 140
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
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 2.5 years ago by
ATpoint
82k • written 2.5 years ago by
suzanne rein
▴ 10
11
votes
3
replies
997
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
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
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
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
29
replies
9.9k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
11
votes
15
replies
2.9k
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
24
replies
5.5k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 520
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
7
replies
1.3k
views
Can two mates have different file size?
sequencing
fastq
5.8 years ago by
marongiu.luigi
▴ 710
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
mra8187
▴ 20
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
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
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
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
25
replies
3.6k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
Za
▴ 140
10
votes
6
replies
2.9k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 14 months ago by
Ram
43k • written 9.0 years ago by
lait
▴ 180
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
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
6
replies
993
views
RNA seq, secreted protein
protein
gene
secreted
updated 9 months ago by
Joe
21k • written 17 months ago by
Rob
▴ 170
10
votes
1
reply
3.5k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 21 months ago by
Ram
43k • written 9.0 years ago by
Niek De Klein
★ 2.6k
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
15
replies
6.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 14 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
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
11 months ago by
Chris
▴ 280
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
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by
yoshifumimiya
▴ 50
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 11 months ago by
Ram
43k • written 4.3 years ago by
gable_works
▴ 50
1,000 results • Page
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Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
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142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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by
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★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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