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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
12
votes
17
replies
4.0k
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
5.6 years ago by
anonymous1192976466
▴ 50
12
votes
4
replies
493
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
15 days ago by
Rafael Soler
★ 1.2k
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp
genotyping
updated 11.7 years ago by
Lars Juhl Jensen
11k • written 12.1 years ago by
Pri
▴ 20
12
votes
8
replies
2.7k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
6.3 years ago by
statfa
▴ 720
12
votes
13
replies
2.2k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 5 months ago by
Ram
39k • written 7.9 years ago by
sarathkurichiyil
• 0
11
votes
22
replies
3.0k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.1 years ago by
RNAseqer
▴ 240
11
votes
10
replies
9.8k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 17 months ago by
Ram
39k • written 8.8 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
1.0k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
2.9 years ago by
screadore
▴ 20
11
votes
2
replies
1.3k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
3.8 years ago by
WUSCHEL
▴ 720
11
votes
9
replies
2.1k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 5 months ago by
Ram
39k • written 8.0 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
6
replies
3.3k
views
bcftools isec -n operators
bcftools
intersect
updated 21 months ago by
Ram
39k • written 3.4 years ago by
Begonia_pavonina
▴ 100
11
votes
7
replies
3.0k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
6.5 years ago by
CF
▴ 50
11
votes
10
replies
5.1k
views
Best mapping software to generate BAM file
BAM
mapping
updated 5.5 years ago by
Biostar
20 • written 5.7 years ago by
Anand Rao
▴ 560
11
votes
10
replies
2.3k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.0 years ago by
plebaninora
• 0
11
votes
5
replies
916
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 18 months ago by
ATpoint
72k • written 18 months ago by
suzanne rein
▴ 10
11
votes
4
replies
2.4k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 6.9 years ago by
Biostar
20 • written 7.1 years ago by
William
★ 5.2k
11
votes
11
replies
4.8k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
5.3 years ago by
ishackm
▴ 110
11
votes
29
replies
8.3k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 19 months ago by
Ram
39k • written 9.0 years ago by
Parham
★ 1.6k
11
votes
11
replies
676
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
3.1 years ago by
lokeshp14cs24
• 0
11
votes
6
replies
5.7k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
5.9 years ago by
Jokhe
▴ 130
11
votes
10
replies
1.3k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 6.7 years ago by
Biostar
20 • written 6.7 years ago by
Farbod
★ 3.4k
11
votes
15
replies
2.4k
views
How do I get the read counts for a specific exon
bam
exon
updated 5.2 years ago by
Ram
39k • written 5.2 years ago by
b10hazard
▴ 30
11
votes
11
replies
2.4k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 7.0 years ago by
Biostar
20 • written 7.0 years ago by
12021560-040
▴ 70
11
votes
24
replies
4.2k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.1 years ago by
williamsbrian5064
▴ 470
10
votes
8
replies
5.7k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 11.7 years ago by
Neilfws
49k • written 11.7 years ago by
Liyf
▴ 300
10
votes
4
replies
1.0k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
2.4 years ago by
dare_devil
★ 3.1k
10
votes
11
replies
4.2k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
9.3 years ago by
inadamj
▴ 60
10
votes
5
replies
6.5k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 9 months ago by
Ram
39k • written 7.8 years ago by
seta
★ 1.8k
10
votes
21
replies
2.4k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.8 years ago by
Biostar
20 • written 3.9 years ago by
Miguel
▴ 10
10
votes
13
replies
5.2k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
6.3 years ago by
Vasu
▴ 720
10
votes
7
replies
952
views
Can two mates have different file size?
sequencing
fastq
4.8 years ago by
marongiu.luigi
▴ 680
10
votes
7
replies
971
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
5.1 years ago by
mhyunjunkang
▴ 110
10
votes
7
replies
3.3k
views
What is Pathway Analysis?
pathway
analysis
ontology
database
tools
7.1 years ago by
Pranavathiyani G
▴ 330
10
votes
9
replies
1.6k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
5.0 years ago by
Angelique
▴ 10
10
votes
2
replies
2.6k
views
Standalone Blast Issue
blast
11.0 years ago by
chlazaris
• 0
10
votes
2
replies
380
views
any script that can do this task
shell-script
updated 14 months ago by
Ram
39k • written 14 months ago by
Confused_human
▴ 10
10
votes
14
replies
3.8k
views
ATAC-seq data and deepTools: Small detail with impact on output
deeptools
ATACseq
bigwig
readlength
Forum
updated 3.3 years ago by
ATpoint
72k • written 3.3 years ago by
gable_works
▴ 50
10
votes
19
replies
2.6k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.0 years ago by
GenoMax
129k • written 2.0 years ago by
matt
▴ 20
10
votes
8
replies
1.5k
views
File Format - Fasta
sequence
7.2 years ago by
Gabe Anderson
▴ 10
10
votes
5
replies
5.2k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 9.3 years ago by
Biostar
20 • written 12.1 years ago by
Arun
2.4k
10
votes
11
replies
8.3k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 12 months ago by
Ram
39k • written 8.2 years ago by
SheelS
▴ 40
10
votes
1
reply
3.8k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 9.5 years ago by
Biostar
20 • written 10.2 years ago by
Ashutosh Pandey
12k
10
votes
15
replies
5.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 9 weeks ago by
Ram
39k • written 4.7 years ago by
marongiu.luigi
▴ 680
10
votes
8
replies
1.9k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 11 months ago by
Ram
39k • written 8.2 years ago by
friasoler
▴ 30
10
votes
5
replies
2.3k
views
error with samtools
RNA-Seq
updated 6.3 years ago by
Biostar
20 • written 6.4 years ago by
mra8187
▴ 20
10
votes
11
replies
1.3k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
4.4 years ago by
Chaimaa
▴ 260
10
votes
23
replies
1.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.5 years ago by
GenoMax
129k • written 5.5 years ago by
Farbod
★ 3.4k
10
votes
10
replies
3.3k
views
Parameter optimization STAR
RNA-Seq
5.3 years ago by
XBria
▴ 90
10
votes
15
replies
5.5k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
6.5 years ago by
Farbod
★ 3.4k
10
votes
25
replies
2.7k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.9 years ago by
Biostar
20 • written 4.9 years ago by
Za
▴ 140
1,000 results • Page
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Answer: RNAseq Data and Pipeline
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Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
Answer: Salmon Index
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Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index
by
ashleymb1116
• 0
Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
Comment: Query qbout single cell sequencing
by
Ram
39k
Show us your exact cellranger and STARsolo commands, the full output to STARsolo as well as your thoughts on why it's not working for you.
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