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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
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
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.3 years ago by
star
▴ 350
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
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
10
replies
4.2k
views
Speed up BLASTp vs NCBI nr database
blast
8.0 years ago by
biotech
▴ 570
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
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 9.8 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
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
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
11
replies
1.1k
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
4.1 years ago by
lokeshp14cs24
• 0
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
6.3k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.9 years ago by
Jokhe
▴ 140
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
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
3
replies
1000
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
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
7.5 years ago by
CF
▴ 50
11
votes
5
replies
1.4k
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
24
replies
5.5k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.1 years ago by
williamsbrian5064
▴ 520
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
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.9 years ago by
plebaninora
• 0
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
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
43k • written 6.2 years ago by
b10hazard
▴ 30
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 7.7 years ago by
Biostar
20 • written 7.7 years ago by
Farbod
★ 3.4k
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
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
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
8
replies
1.8k
views
File Format - Fasta
sequence
8.2 years ago by
Gabe Anderson
▴ 10
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
998
views
RNA seq, secreted protein
protein
gene
secreted
updated 9 months ago by
Joe
21k • written 17 months ago by
Rob
▴ 170
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
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
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
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
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
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
2
replies
2.8k
views
Standalone Blast Issue
blast
12.0 years ago by
chlazaris
• 0
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
1,000 results • Page
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Recent Votes
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How To Convert List Of Entrez Ids Into Gene Name
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Comment: What marks a De-Novo Genome assembly as FAILED?
A: How to extract specific chromosome from vcf file
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Recent Replies
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 210
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
Klaus S
▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
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