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Limit : all time
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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
12
votes
10
replies
3.9k
views
Speed up BLASTp vs NCBI nr database
blast
7.3 years ago by
biotech
▴ 570
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
5.9 years ago by
anonymous1192976466
▴ 50
12
votes
8
replies
874
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
12
votes
11
replies
3.0k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.1 years ago by
Lars Juhl Jensen
11k • written 12.5 years ago by
Pri
▴ 20
11
votes
22
replies
3.3k
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
1.1k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
3.2 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
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
▴ 560
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
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
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
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
7
replies
3.1k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
6.9 years ago by
CF
▴ 50
11
votes
11
replies
787
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
3.4 years ago by
lokeshp14cs24
• 0
11
votes
6
replies
3.5k
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
4
replies
2.5k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 7.2 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
5
replies
1.0k
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 21 months ago by
ATpoint
76k • written 21 months ago by
suzanne rein
▴ 10
11
votes
10
replies
2.5k
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
29
replies
8.7k
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
24
replies
4.6k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.4 years ago by
williamsbrian5064
▴ 480
10
votes
8
replies
5.8k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.0 years ago by
Neilfws
49k • written 12.0 years ago by
Liyf
▴ 300
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
7
replies
3.4k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 3 months ago by
Ram
40k • written 7.4 years ago by
Pranavathiyani G
▴ 330
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
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
15
replies
5.7k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
6.8 years ago by
Farbod
★ 3.4k
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
11
replies
4.4k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
9.6 years ago by
inadamj
▴ 60
10
votes
11
replies
8.6k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 15 months ago by
Ram
40k • written 8.5 years ago by
SheelS
▴ 40
10
votes
2
replies
445
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
23
replies
2.0k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.8 years ago by
GenoMax
134k • written 5.8 years ago by
Farbod
★ 3.4k
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
6
replies
683
views
RNA seq, secreted protein
protein
gene
secreted
updated 7 weeks ago by
Joe
21k • written 9 months ago by
Rob
▴ 160
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
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
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
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
8
replies
1.6k
views
File Format - Fasta
sequence
7.5 years ago by
Gabe Anderson
▴ 10
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
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
2.0k
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
1
reply
3.8k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 9.8 years ago by
Biostar
20 • written 10.5 years ago by
Ashutosh Pandey
12k
10
votes
25
replies
3.0k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.2 years ago by
Biostar
20 • written 5.2 years ago by
Za
▴ 140
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
10
votes
2
replies
2.7k
views
Standalone Blast Issue
blast
11.3 years ago by
chlazaris
• 0
10
votes
7
replies
1.0k
views
Can two mates have different file size?
sequencing
fastq
5.1 years ago by
marongiu.luigi
▴ 690
1,000 results • Page
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Recent Votes
Comment: Salmon index not progressing
Answer: Adding a control sample to bulk RNA-seq
Comment: Adding a control sample to bulk RNA-seq
Comment: kallisto normalized TPM values without bootstraps
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Identify Alternative Splicing Event using exon and junction count table
Comment: Salmon index not progressing
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Recent Replies
Comment: Salmon index not progressing
by
camillab.
▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★ 2.5k
you expect to have aneuploidy only in the knockout?
Comment: STAR index not working
by
camillab.
▴ 130
thank you! I am following GenoMax suggestion and I am trying with `salmon` but it is stuck as well. it's not making any progress.....
Comment: Scanning for ultra-hot topics in science via pubmed, or using other tools
by
LauferVA
3.7k
@genomax , thank you. this is a really great start. i will likely use a python based approach, but other than that, i think ill proceed e…
Comment: OMA in AWS cloud
by
Ram
40k
> if it is possible. Yes, most things are possible on AWS. > I didn't find anything in the web. I *highly* **highly** doubt that.
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