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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
12
votes
28
replies
2.7k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
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
6.5 years ago by
anonymous1192976466
▴ 50
12
votes
8
replies
1.3k
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 19 months ago by
Matthias Zepper
4.5k • written 19 months ago by
A_heath
▴ 160
12
votes
11
replies
3.2k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.7 years ago by
Lars Juhl Jensen
11k • written 13.0 years ago by
Pri
▴ 20
12
votes
14
replies
5.7k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.2 years ago by
star
▴ 350
12
votes
12
replies
4.9k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 10.4 years ago by
Istvan Albert
100k • written 10.4 years ago by
biolab
★ 1.4k
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.3 years ago by
John
13k
12
votes
13
replies
2.7k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 16 months ago by
Ram
43k • written 8.8 years ago by
sarathkurichiyil
• 0
12
votes
21
replies
3.2k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
Miguel
▴ 30
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 17 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 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
3.8 years ago by
screadore
▴ 20
11
votes
2
replies
1.5k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
4.7 years ago by
WUSCHEL
▴ 750
11
votes
3
replies
956
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
10
replies
5.8k
views
Best mapping software to generate BAM file
BAM
mapping
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
Anand Rao
▴ 630
11
votes
6
replies
3.2k
views
Understanding Supplementary reads.
Bowtie2
MEM
BWA
Dragen
updated 2.2 years ago by
Istvan Albert
100k • written 2.2 years ago by
kiran
▴ 10
11
votes
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 16 months ago by
Ram
43k • written 8.9 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
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 7.8 years ago by
Biostar
20 • written 8.0 years ago by
William
★ 5.3k
11
votes
29
replies
9.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
11
votes
11
replies
5.6k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
6.2 years ago by
ishackm
▴ 110
11
votes
24
replies
5.4k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 510
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 2.4 years ago by
ATpoint
82k • written 2.4 years ago by
suzanne rein
▴ 10
11
votes
11
replies
2.7k
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
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
6.8 years ago by
Jokhe
▴ 140
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 7.6 years ago by
Farbod
★ 3.4k
11
votes
15
replies
2.8k
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
11
replies
1.0k
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
4.0 years ago by
lokeshp14cs24
• 0
10
votes
8
replies
6.1k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.6 years ago by
Neilfws
49k • written 12.6 years ago by
Liyf
▴ 300
10
votes
7
replies
1.2k
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
6.0 years ago by
mhyunjunkang
▴ 110
10
votes
3
replies
1.4k
views
how to create new file
r
updated 7.5 years ago by
GenoMax
141k • written 7.5 years ago by
forever
▴ 80
10
votes
25
replies
3.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
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 10 months ago by
Ram
43k • written 4.2 years ago by
gable_works
▴ 50
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.2 years ago by
Biostar
20 • written 7.4 years ago by
mra8187
▴ 20
10
votes
8
replies
2.3k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 22 months ago by
Ram
43k • written 9.1 years ago by
friasoler
▴ 50
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
10
votes
8
replies
1.7k
views
File Format - Fasta
sequence
8.1 years ago by
Gabe Anderson
▴ 10
10
votes
15
replies
6.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 13 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
10
votes
1
reply
4.0k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 10.4 years ago by
Biostar
20 • written 11.1 years ago by
Ashutosh Pandey
12k
10
votes
6
replies
975
views
RNA seq, secreted protein
protein
gene
secreted
updated 8 months ago by
Joe
21k • written 16 months ago by
Rob
▴ 170
10
votes
11
replies
4.7k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
10.2 years ago by
inadamj
▴ 60
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.4 years ago by
Farbod
★ 3.4k
10
votes
6
replies
2.9k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 13 months ago by
Ram
43k • written 8.9 years ago by
lait
▴ 180
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
10
votes
5
replies
7.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 20 months ago by
Ram
43k • written 8.7 years ago by
seta
★ 1.9k
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.2 years ago by
XBria
▴ 90
10
votes
1
reply
3.5k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 20 months ago by
Ram
43k • written 8.9 years ago by
Niek De Klein
★ 2.6k
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
2
replies
600
views
any script that can do this task
shell-script
updated 2.1 years ago by
Ram
43k • written 2.1 years ago by
Confused_human
▴ 20
1,000 results • Page
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Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
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by
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
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I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
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Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
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install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
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Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
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bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
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starswillfade
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I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
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