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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
6.5 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 12.6 years ago by
Lars Juhl Jensen
11k • written 13.0 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
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.3 years ago by
John
13k
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
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 15 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
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
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
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
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
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
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
24
replies
5.4k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 510
11
votes
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.9 years ago by
plebaninora
• 0
11
votes
3
replies
952
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
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
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
7.4 years ago by
CF
▴ 50
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
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
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
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
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
10 months ago by
Chris
▴ 260
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
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
973
views
RNA seq, secreted protein
protein
gene
secreted
updated 8 months ago by
Joe
21k • written 16 months ago by
Rob
▴ 170
10
votes
6
replies
2.8k
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
9.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
SheelS
▴ 40
10
votes
11
replies
1.6k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
5.3 years ago by
Chaimaa
▴ 260
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.2 years ago by
XBria
▴ 90
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
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
1,000 results • Page
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Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Comment: To get p-values for the TPM
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VITALA
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yes i want what rsem does
Comment: alignment result
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Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
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The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
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Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
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duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
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Thanks for the input. I'll continue to think of more ideas that may be achievable.
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