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122,199 results • Page
645 of 2444
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0
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0
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How can I make multiple taxID queries using qblast and store multiple blast handles using NCBIXML?
NCBIXML
qblast
python
biopython
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
oseias.rf.junior
• 0
0
votes
1
reply
869
views
Tools for SNPs and Indels (RNA seq)
SNPs
Oxford
RNA-seq
Nanopore
INDELS
updated 4.5 years ago by
Manisha Sapre
• 0 • written 4.5 years ago by
mailard
▴ 30
0
votes
0
replies
876
views
Job:
Postdoc Fellow @ New York: Long Reads, Alternative Splicing and Human Diseases
assembly
sequencing
RNA-Seq
4.5 years ago by
fanggang
▴ 120
118
votes
66
replies
54k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 2.7 years ago by
Ram
45k • written 7.4 years ago by
ATpoint
90k
0
votes
2
replies
1.5k
views
CNVkit result interpretation
results
cnv
interpretation
updated 4.5 years ago by
brunobsouzaa
▴ 840 • written 4.5 years ago by
enes
▴ 40
2
votes
6
replies
2.3k
views
Downloading bacterial genomes: correspondence between ftp ncbi identifiers and the "nucleotide" database
python
ncbi
biopython
updated 4.5 years ago by
vkkodali_ncbi
★ 3.9k • written 4.5 years ago by
Debut
▴ 20
6
votes
6
replies
6.9k
views
Problem with featureCounts using a GTF generated by me
gtf
annotation
rnaseq
updated 4.4 years ago by
Juke34
9.3k • written 4.5 years ago by
arturo.marin
▴ 20
0
votes
1
reply
2.2k
views
MACS2 error in fragment size estimation from paired-end STAR-aligned RNA-seq data
ChIP-Seq
software
alignment
RNA-Seq
error
updated 4.5 years ago by
ATpoint
90k • written 5.4 years ago by
bsaleme
• 0
0
votes
1
reply
1.2k
views
Is there a pipeline for analyzing the chromatin states and describe the process of formation?
chromHMM
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
charlie
• 0
2
votes
1
reply
983
views
jellyfish
HELPPPPPPPPPPP
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
Oumaima
• 0
4
votes
5
replies
1.8k
views
List index out of range
python
varscan
cnvtogenes
4.5 years ago by
Samiah
▴ 10
1
vote
4
replies
1.9k
views
unmapped reads BAM TCGA
unmapped
BAM
read
TCGA
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
Taktak31
• 0
1
vote
2
replies
1.5k
views
How to choose k-mer for the genome size estimation?
Assembly
genome
updated 4.5 years ago by
Oumaima
• 0 • written 4.9 years ago by
524730309
• 0
0
votes
2
replies
1.3k
views
How to calculate PSSM for large batch of proteins?
PSIBLAST
BLAST
PSSM
MACHINELEARNING
4.5 years ago by
aakashy01
• 0
1
vote
4
replies
5.2k
views
How to know if the sample from SRA is trimmed or un-trimmed
FASTQC
NGS
SRA
FASTQ
NCBI
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
FadyNabil
▴ 20
0
votes
0
replies
783
views
About Structural variation genotypes
variants
Structural-variants
variant-calling
genotypes
updated 2.1 years ago by
Ram
45k • written 4.5 years ago by
prasundutta87
▴ 730
6
votes
3
replies
8.3k
views
How to set up bcftools plugins?
BCFTOOLS
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
Filago
▴ 110
12
votes
8
replies
23k
views
Genome assembly N50
Assembly
assembly tools
N50
updated 4.5 years ago by
lieven.sterck
16k • written 7.5 years ago by
Inquisitive8995
▴ 280
3
votes
1
reply
1.4k
views
Fisher exact test in R package
Fisher-test
updated 20 months ago by
Ram
45k • written 4.5 years ago by
Nuglozeh
▴ 10
4
votes
0
replies
1.6k
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
4.5 years ago by
pbpanigrahi
▴ 430
0
votes
1
reply
954
views
Query regarding WGCNA module formation
WGCNA
R
RNA-seq
updated 4.5 years ago by
andres.firrincieli
3.9k • written 4.5 years ago by
microorganism_001
▴ 30
0
votes
1
reply
1.2k
views
Detection of biallelic mutation (inactivation)
somatic
biallelic
mutation
updated 4.5 years ago by
Arsenal
▴ 160 • written 4.5 years ago by
CY
▴ 750
15
votes
10
replies
23k
views
7 follow
How to convert bulk UniProt Id to GO terms/Ids?
Uniprot
RNA-Seq
Assembly
updated 4.5 years ago by
Pratik
★ 1.1k • written 8.8 years ago by
mirzaei86.vahid
▴ 50
1
vote
0
replies
1.3k
views
Colocalization window size
COLOC
eqtl
R
gwas
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
Filago
▴ 110
8
votes
25
replies
5.0k
views
construction of a database
sql
noSQL
neo4j
database
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Debut
▴ 20
2
votes
3
replies
13k
views
Using Seurat function `FindMarkers` to find differentially expressed genes between normal group and treatment group within one specific cell type clu…
Seurat
FindMarkers
scRNA
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
FantasticAI
▴ 60
4
votes
6
replies
14k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 18 months ago by
jared.andrews07
★ 19k • written 6.2 years ago by
cook.675
▴ 250
2
votes
4
replies
1.4k
views
What is the meaning of the name MUMmer ?
Mummerplot
Dna
Alignment
Mummer
Sequence
4.5 years ago by
Student
▴ 30
0
votes
0
replies
780
views
GWAS catalog results as input for Prsice2
Polygenic
SNPs
scoring
risk
GWAS
Genotype
4.5 years ago by
davidenoma
▴ 50
0
votes
3
replies
1.8k
views
Sequence Read Archive (SRA) submission ERROR
submission
rnaseq
sra
updated 4.1 years ago by
annabelle.damerum
• 0 • written 4.5 years ago by
ovariohisterectomia
▴ 40
2
votes
1
reply
941
views
Color protein multiple sequence alignement per secondary structures
multiple
secondary
sequence
alignment
structures
color
4.5 years ago by
ttubiana
▴ 30
0
votes
4
replies
1.4k
views
different padj from DESeq2 when using different contrast input format
DESeq2
RNA-Seq
4.5 years ago by
cwwong13
▴ 40
2
votes
4
replies
1.4k
views
whole tissue and RNA-seq: can I still study specific cell types?
WGCNA
rnaseq
4.5 years ago by
demoraesdiogo2017
▴ 120
0
votes
2
replies
2.0k
views
Converting U to T in my miRNA sequences
RNA-Seq
updated 4.5 years ago by
Pierre Lindenbaum
166k • written 4.5 years ago by
aranyak111
• 0
1
vote
1
reply
1.9k
views
Job:
Bioinformatics Solution Architect @ Elucidata, Cambridge MA (USA)
Cambridge
Boston
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
ben.lubetsky
• 0
0
votes
1
reply
1.3k
views
SICER2 (or EPIC) genomes
Genome
EPIC
ChIP-seq
SICER
Sequencing
updated 4.5 years ago by
ATpoint
90k • written 4.5 years ago by
jjp55
▴ 20
1
vote
3
replies
1.6k
views
circular R plot
r
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
evafinegan
• 0
0
votes
1
reply
1.2k
views
How can i handle the multimapped reads?
assembly
sequencing
alignment
updated 4.5 years ago by
Charlene Hsuan-lin Her
• 0 • written 4.8 years ago by
PK
▴ 130
2
votes
4
replies
1.1k
views
Finding length of multiple fastq.gz files
zcat
Fastq
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
brisbio
▴ 30
5
votes
2
replies
1.8k
views
How to compare cell-type ratios in sc-RNA seq data?
sc-RNA
single-cell
cell-type
4.5 years ago by
sc-ruzafa
▴ 20
2
votes
1
reply
1000
views
Package/script for random DNA generation with a pattern!
DNA
regex
methylation
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.5 years ago by
Parham
★ 1.6k
7
votes
7
replies
14k
views
7 follow
ViennaRNA error: ImportError: No module named _RNA
python
viennrna
updated 3.5 years ago by
JVicers
• 0 • written 11.5 years ago by
tfadgreef
• 0
1
vote
2
replies
1.1k
views
Cytoscape JSON file format and STYLE storage
Cytoscape
Styles
JSON
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
SKY
▴ 60
0
votes
0
replies
877
views
Read group: ID, PU definition and multi-lane (same sample)
multilane
group_read
RG
4.5 years ago by
emma.a
▴ 130
1
vote
1
reply
3.1k
views
ValueError: attempt to get argmax of an empty sequence
mtag
python2
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.5 years ago by
Fede_Santos95
▴ 20
1
vote
0
replies
1.1k
views
calculate LCA with MEGAN UE command line mode for multiple bast files
LCA
line
MEGAN6
command
4.5 years ago by
Mathilde Borg Dahl
▴ 10
2
votes
2
replies
4.1k
views
Reference Genome dna, rm or sm??
unmaksed
Reference
masked
genome
4.5 years ago by
SKY
▴ 60
0
votes
0
replies
808
views
Job:
PhD position: Computational Epigenetics in cancer cell reprogramming
organization
chromatin
3D
analyses
data
image
proecessing
HiCHIP
integrative
OligoSTORM
4.5 years ago by
alessio.zippo
• 0
0
votes
5
replies
1.4k
views
How can I drop the MAPQ info of my sam/bam file?
bam
updated 4.5 years ago by
Carlo Yague
9.0k • written 4.5 years ago by
francois
▴ 90
0
votes
0
replies
904
views
Job:
Senior Bioinformatician (Proteomics, Immunocore, UK)
proteomics
UK
immunocore
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
enric.serra
• 0
122,199 results • Page
645 of 2444
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Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
You can check the read lengths of each file to determine which one is the R1 and which is the R2. Also, check the 10x protocol version they…
Comment: Subsetting before QC in Spatial Transcriptomics
by
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Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
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▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
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▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
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★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat
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yura.grabovska
▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays
by
yura.grabovska
▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
michael.ante
★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome?
by
dthorbur
★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
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by
2411110159
• 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
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by
2411110159
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Very helpful!
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